Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters
Identifieur interne : 000145 ( Ncbi/Merge ); précédent : 000144; suivant : 000146Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters
Auteurs : Paul Gagniuc [Roumanie] ; Constantin Ionescu-Tirgoviste [Roumanie]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
English descriptors
- KwdEn :
- Animals, Arabidopsis (genetics), Classification, Databases, Genetic, Drosophila melanogaster (genetics), Gene Expression Regulation (genetics), Genome (genetics), Humans, Neural Networks (Computer), Organ Specificity (genetics), Oryza (genetics), Phylogeny, Promoter Regions, Genetic (genetics), Species Specificity.
- MESH :
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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PMC:3549790Le document en format XML
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<author><name sortKey="Ionescu Tirgoviste, Constantin" sort="Ionescu Tirgoviste, Constantin" uniqKey="Ionescu Tirgoviste C" first="Constantin" last="Ionescu-Tirgoviste">Constantin Ionescu-Tirgoviste</name>
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<term>Drosophila melanogaster (genetics)</term>
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<term>Genome (genetics)</term>
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<term>Organ Specificity (genetics)</term>
<term>Oryza (genetics)</term>
<term>Phylogeny</term>
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<term>Species Specificity</term>
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<term>Drosophila melanogaster</term>
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<term>Genome</term>
<term>Organ Specificity</term>
<term>Oryza</term>
<term>Promoter Regions, Genetic</term>
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<term>Classification</term>
<term>Databases, Genetic</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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?</p>
</sec>
<sec><title>Results</title>
<p>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 <italic>Arabidopsis thaliana</italic>
, <italic>Drosophila melanogaster</italic>
, <italic>Homo sapiens</italic>
and <italic>Oryza sativa</italic>
, and a more extensive analysis of tissue-specific promoters in humans. We observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, we found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, we also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. Our conclusions are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence.</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
</div>
</front>
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<double pmid="23020586"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters</title>
<author><name sortKey="Gagniuc, Paul" sort="Gagniuc, Paul" uniqKey="Gagniuc P" first="Paul" last="Gagniuc">Paul Gagniuc</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Institute of Genetics, University of Bucharest, Bucharest 060101, Romania</nlm:aff>
<country xml:lang="fr">Roumanie</country>
<wicri:regionArea>Institute of Genetics, University of Bucharest, Bucharest 060101</wicri:regionArea>
<wicri:noRegion>Bucharest 060101</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ionescu Tirgoviste, Constantin" sort="Ionescu Tirgoviste, Constantin" uniqKey="Ionescu Tirgoviste C" first="Constantin" last="Ionescu-Tirgoviste">Constantin Ionescu-Tirgoviste</name>
<affiliation wicri:level="1"><nlm:aff id="I2">National Institute of Diabetes, Nutrition and Metabolic Diseases “N.C. Paulescu”, Bucharest, Romania</nlm:aff>
<country xml:lang="fr">Roumanie</country>
<wicri:regionArea>National Institute of Diabetes, Nutrition and Metabolic Diseases “N.C. Paulescu”, Bucharest</wicri:regionArea>
<wicri:noRegion>Bucharest</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">23020586</idno>
<idno type="pmc">3549790</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549790</idno>
<idno type="RBID">PMC:3549790</idno>
<idno type="doi">10.1186/1471-2164-13-512</idno>
<date when="2012">2012</date>
<idno type="wicri:Area/Pmc/Corpus">000099</idno>
<idno type="wicri:Area/Pmc/Curation">000099</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000108</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters</title>
<author><name sortKey="Gagniuc, Paul" sort="Gagniuc, Paul" uniqKey="Gagniuc P" first="Paul" last="Gagniuc">Paul Gagniuc</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Institute of Genetics, University of Bucharest, Bucharest 060101, Romania</nlm:aff>
<country xml:lang="fr">Roumanie</country>
<wicri:regionArea>Institute of Genetics, University of Bucharest, Bucharest 060101</wicri:regionArea>
<wicri:noRegion>Bucharest 060101</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ionescu Tirgoviste, Constantin" sort="Ionescu Tirgoviste, Constantin" uniqKey="Ionescu Tirgoviste C" first="Constantin" last="Ionescu-Tirgoviste">Constantin Ionescu-Tirgoviste</name>
<affiliation wicri:level="1"><nlm:aff id="I2">National Institute of Diabetes, Nutrition and Metabolic Diseases “N.C. Paulescu”, Bucharest, Romania</nlm:aff>
<country xml:lang="fr">Roumanie</country>
<wicri:regionArea>National Institute of Diabetes, Nutrition and Metabolic Diseases “N.C. Paulescu”, Bucharest</wicri:regionArea>
<wicri:noRegion>Bucharest</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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?</p>
</sec>
<sec><title>Results</title>
<p>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 <italic>Arabidopsis thaliana</italic>
, <italic>Drosophila melanogaster</italic>
, <italic>Homo sapiens</italic>
and <italic>Oryza sativa</italic>
, and a more extensive analysis of tissue-specific promoters in humans. We observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, we found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, we also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. Our conclusions are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence.</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
</div>
</front>
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<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.</title>
<author><name sortKey="Gagniuc, Paul" sort="Gagniuc, Paul" uniqKey="Gagniuc P" first="Paul" last="Gagniuc">Paul Gagniuc</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Genetics, University of Bucharest, Bucharest 060101, Romania. paul_gagniuc@acad.ro</nlm:affiliation>
<country xml:lang="fr">Roumanie</country>
<wicri:regionArea>Institute of Genetics, University of Bucharest, Bucharest 060101</wicri:regionArea>
<wicri:noRegion>Bucharest 060101</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ionescu Tirgoviste, Constantin" sort="Ionescu Tirgoviste, Constantin" uniqKey="Ionescu Tirgoviste C" first="Constantin" last="Ionescu-Tirgoviste">Constantin Ionescu-Tirgoviste</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2012">2012</date>
<idno type="doi">10.1186/1471-2164-13-512</idno>
<idno type="RBID">pubmed:23020586</idno>
<idno type="pmid">23020586</idno>
<idno type="wicri:Area/PubMed/Corpus">000025</idno>
<idno type="wicri:Area/PubMed/Curation">000025</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000025</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.</title>
<author><name sortKey="Gagniuc, Paul" sort="Gagniuc, Paul" uniqKey="Gagniuc P" first="Paul" last="Gagniuc">Paul Gagniuc</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Genetics, University of Bucharest, Bucharest 060101, Romania. paul_gagniuc@acad.ro</nlm:affiliation>
<country xml:lang="fr">Roumanie</country>
<wicri:regionArea>Institute of Genetics, University of Bucharest, Bucharest 060101</wicri:regionArea>
<wicri:noRegion>Bucharest 060101</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ionescu Tirgoviste, Constantin" sort="Ionescu Tirgoviste, Constantin" uniqKey="Ionescu Tirgoviste C" first="Constantin" last="Ionescu-Tirgoviste">Constantin Ionescu-Tirgoviste</name>
</author>
</analytic>
<series><title level="j">BMC genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2012" type="published">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Arabidopsis (genetics)</term>
<term>Classification</term>
<term>Databases, Genetic</term>
<term>Drosophila melanogaster (genetics)</term>
<term>Gene Expression Regulation (genetics)</term>
<term>Genome (genetics)</term>
<term>Humans</term>
<term>Neural Networks (Computer)</term>
<term>Organ Specificity (genetics)</term>
<term>Oryza (genetics)</term>
<term>Phylogeny</term>
<term>Promoter Regions, Genetic (genetics)</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Drosophila melanogaster</term>
<term>Gene Expression Regulation</term>
<term>Genome</term>
<term>Organ Specificity</term>
<term>Oryza</term>
<term>Promoter Regions, Genetic</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Classification</term>
<term>Databases, Genetic</term>
<term>Humans</term>
<term>Neural Networks (Computer)</term>
<term>Phylogeny</term>
<term>Species Specificity</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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?</div>
</front>
</TEI>
</pubmed>
</double>
</record>
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