Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.
Identifieur interne : 000025 ( PubMed/Corpus ); précédent : 000024; suivant : 000026Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.
Auteurs : Paul Gagniuc ; Constantin Ionescu-TirgovisteSource :
- 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?
DOI: 10.1186/1471-2164-13-512
PubMed: 23020586
Links to Exploration step
pubmed:23020586Le document en format XML
<record><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><nlm:affiliation>Institute of Genetics, University of Bucharest, Bucharest 060101, Romania. paul_gagniuc@acad.ro</nlm:affiliation></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></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><nlm:affiliation>Institute of Genetics, University of Bucharest, Bucharest 060101, Romania. paul_gagniuc@acad.ro</nlm:affiliation></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><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">23020586</PMID><DateCreated><Year>2013</Year><Month>01</Month><Day>22</Day></DateCreated><DateCompleted><Year>2013</Year><Month>06</Month><Day>11</Day></DateCompleted><DateRevised><Year>2015</Year><Month>11</Month><Day>19</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><PubDate><Year>2012</Year></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.</ArticleTitle><Pagination><MedlinePgn>512</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-13-512</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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?</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">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 Arabidopsis thaliana, Drosophila melanogaster, Homo sapiens and Oryza sativa, 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.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gagniuc</LastName><ForeName>Paul</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institute of Genetics, University of Bucharest, Bucharest 060101, Romania. paul_gagniuc@acad.ro</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ionescu-Tirgoviste</LastName><ForeName>Constantin</ForeName><Initials>C</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>09</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Gene. 1999 Oct 18;239(1):15-27</RefSource><PMID Version="1">10571030</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25</RefSource><PMID Version="1">22140104</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2000 Sep;26(1):61-3</RefSource><PMID Version="1">10973249</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2000 Nov 1;28(21):4083-9</RefSource><PMID Version="1">11058103</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome 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