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Large-scale structural analysis of the core promoter in mammalian and plant genomes

Kobe Florquin (UGent) , Yvan Saeys (UGent) , Sven Degroeve (UGent) , Pierre Rouzé (UGent) and Yves Van de Peer (UGent)
(2005) NUCLEIC ACIDS RESEARCH. 33(13). p.4255-4264
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Abstract
DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.
Keywords
DNA, DEPENDENT TRANSCRIPTION, TATA BOX, CPG-ISLANDS, GENE-EXPRESSION, BOX-BINDING PROTEIN, RNA-POLYMERASE-II, TRANSCRIPTIONAL START SITES, SEQUENCE, ELEMENT

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MLA
Florquin, Kobe, Yvan Saeys, Sven Degroeve, et al. “Large-scale Structural Analysis of the Core Promoter in Mammalian and Plant Genomes.” NUCLEIC ACIDS RESEARCH 33.13 (2005): 4255–4264. Print.
APA
Florquin, K., Saeys, Y., Degroeve, S., Rouzé, P., & Van de Peer, Y. (2005). Large-scale structural analysis of the core promoter in mammalian and plant genomes. NUCLEIC ACIDS RESEARCH, 33(13), 4255–4264.
Chicago author-date
Florquin, Kobe, Yvan Saeys, Sven Degroeve, Pierre Rouzé, and Yves Van de Peer. 2005. “Large-scale Structural Analysis of the Core Promoter in Mammalian and Plant Genomes.” Nucleic Acids Research 33 (13): 4255–4264.
Chicago author-date (all authors)
Florquin, Kobe, Yvan Saeys, Sven Degroeve, Pierre Rouzé, and Yves Van de Peer. 2005. “Large-scale Structural Analysis of the Core Promoter in Mammalian and Plant Genomes.” Nucleic Acids Research 33 (13): 4255–4264.
Vancouver
1.
Florquin K, Saeys Y, Degroeve S, Rouzé P, Van de Peer Y. Large-scale structural analysis of the core promoter in mammalian and plant genomes. NUCLEIC ACIDS RESEARCH. 2005;33(13):4255–64.
IEEE
[1]
K. Florquin, Y. Saeys, S. Degroeve, P. Rouzé, and Y. Van de Peer, “Large-scale structural analysis of the core promoter in mammalian and plant genomes,” NUCLEIC ACIDS RESEARCH, vol. 33, no. 13, pp. 4255–4264, 2005.
@article{329232,
  abstract     = {DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.},
  author       = {Florquin, Kobe and Saeys, Yvan and Degroeve, Sven and Rouzé, Pierre and Van de Peer, Yves},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {DNA,DEPENDENT TRANSCRIPTION,TATA BOX,CPG-ISLANDS,GENE-EXPRESSION,BOX-BINDING PROTEIN,RNA-POLYMERASE-II,TRANSCRIPTIONAL START SITES,SEQUENCE,ELEMENT},
  language     = {eng},
  number       = {13},
  pages        = {4255--4264},
  title        = {Large-scale structural analysis of the core promoter in mammalian and plant genomes},
  url          = {http://dx.doi.org/10.1093/nar/gki737},
  volume       = {33},
  year         = {2005},
}

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