Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters
Identifieur interne : 000099 ( Pmc/Corpus ); précédent : 000098; suivant : 000100Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters
Auteurs : Paul Gagniuc ; Constantin Ionescu-TirgovisteSource :
- BMC Genomics [ 1471-2164 ] ; 2012.
Abstract
The main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. Generally, promoters have been classified in two major classes, namely TATA and CpG. Nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. Accordingly, we tried to ask ourselves some fundamental questions: Why certain genes have an overall predisposition for higher gene expression levels than others? What causes such a predisposition? Is there a structural relationship of these sequences in different tissues? Is there a strong phylogenetic relationship between promoters of closely related species?
In order to gain valuable insights into different promoter regions, we obtained a series of image-based patterns which allowed us to identify 10 generic classes of promoters. A comprehensive analysis was undertaken for promoter sequences from
To fully understand the connections between gene promoters and gene expression, we analyzed thousands of promoter sequences using our Kappa Index of Coincidence method and a specialized Optical Character Recognition (OCR) neural network. Under our criteria, 10 classes of promoters were detected. In addition, the existence of “transitional” promoters suggests that there is an evolutionary weighted continuum between classes, depending perhaps upon changes in their gene products.
Url:
DOI: 10.1186/1471-2164-13-512
PubMed: 23020586
PubMed Central: 3549790
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