Exploring the characteristics of sequence elements in proximal promoters of human genes.
Identifieur interne : 003065 ( Main/Curation ); précédent : 003064; suivant : 003066Exploring the characteristics of sequence elements in proximal promoters of human genes.
Auteurs : Minou Bina [États-Unis] ; Phillip Wyss ; Wenhui Ren ; Wojciech Szpankowski ; Elizabeth Thomas ; Ranjit Randhawa ; Sreedeepti Reddy ; Priya M. John ; Elsie I. Pares-Matos ; Arnold Stein ; Hao Xu ; Sheryl A. LazarusSource :
- Genomics [ 0888-7543 ] ; 2004.
Descripteurs français
- KwdFr :
- Bases de données génétiques, Biologie informatique, Données de séquences moléculaires, Facteurs de transcription (métabolisme), Humains, Liaison aux protéines, Régions 5' non traduites (génétique), Régions promotrices (génétique) (génétique), Régulation de l'expression des gènes, Site d'initiation de la transcription, Sites de fixation, Séquence nucléotidique, Transcription génétique (génétique), Éléments de réponse (génétique).
- MESH :
- génétique : Régions 5' non traduites, Régions promotrices (génétique), Transcription génétique, Éléments de réponse.
- métabolisme : Facteurs de transcription.
- Bases de données génétiques, Biologie informatique, Données de séquences moléculaires, Humains, Liaison aux protéines, Régulation de l'expression des gènes, Site d'initiation de la transcription, Sites de fixation, Séquence nucléotidique.
English descriptors
- KwdEn :
- 5' Untranslated Regions (genetics), Base Sequence, Binding Sites, Computational Biology, Databases, Genetic, Gene Expression Regulation, Humans, Molecular Sequence Data, Promoter Regions, Genetic (genetics), Protein Binding, Response Elements (genetics), Transcription Factors (metabolism), Transcription Initiation Site, Transcription, Genetic (genetics).
- MESH :
- chemical , genetics : 5' Untranslated Regions.
- genetics : Promoter Regions, Genetic, Response Elements, Transcription, Genetic.
- chemical , metabolism : Transcription Factors.
- Base Sequence, Binding Sites, Computational Biology, Databases, Genetic, Gene Expression Regulation, Humans, Molecular Sequence Data, Protein Binding, Transcription Initiation Site.
Abstract
Central to reconstruction of cis-regulatory networks is identification and classification of naturally occurring transcription factor-binding sites according to the genes that they control. We have examined salient characteristics of 9-mers that occur in various orders and combinations in the proximal promoters of human genes. In evaluations of a dataset derived with respect to experimentally defined transcription initiation sites, in some cases we observed a clear correspondence of highly ranked 9-mers with protein-binding sites in genomic DNA. Evaluations of the larger dataset, derived with respect to the 5' end of human ESTs, revealed that a subset of the highly ranked 9-mers corresponded to sites for several known transcription factor families (including CREB, ETS, EGR-1, SP1, KLF, MAZ, HIF-1, and STATs) that play important roles in the regulation of vertebrate genes. We identified several highly ranked CpG-containing 9-mers, defining sites for interactions with the CREB and ETS families of proteins, and identified potential target genes for these proteins. The results of the studies imply that the CpG-containing transcription factor-binding sites regulate the expression of genes with important roles in pathways leading to cell-type-specific gene expression and pathways controlled by the complex networks of signaling systems.
DOI: 10.1016/j.ygeno.2004.08.013
PubMed: 15533710
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pubmed:15533710Le document en format XML
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John</name></author><author><name sortKey="Pares Matos, Elsie I" sort="Pares Matos, Elsie I" uniqKey="Pares Matos E" first="Elsie I" last="Pares-Matos">Elsie I. Pares-Matos</name></author><author><name sortKey="Stein, Arnold" sort="Stein, Arnold" uniqKey="Stein A" first="Arnold" last="Stein">Arnold Stein</name></author><author><name sortKey="Xu, Hao" sort="Xu, Hao" uniqKey="Xu H" first="Hao" last="Xu">Hao Xu</name></author><author><name sortKey="Lazarus, Sheryl A" sort="Lazarus, Sheryl A" uniqKey="Lazarus S" first="Sheryl A" last="Lazarus">Sheryl A. Lazarus</name></author></analytic><series><title level="j">Genomics</title><idno type="ISSN">0888-7543</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>5' Untranslated Regions (genetics)</term><term>Base Sequence</term><term>Binding Sites</term><term>Computational Biology</term><term>Databases, Genetic</term><term>Gene Expression Regulation</term><term>Humans</term><term>Molecular Sequence Data</term><term>Promoter Regions, Genetic (genetics)</term><term>Protein Binding</term><term>Response Elements (genetics)</term><term>Transcription Factors (metabolism)</term><term>Transcription Initiation Site</term><term>Transcription, Genetic (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Données de séquences moléculaires</term><term>Facteurs de transcription (métabolisme)</term><term>Humains</term><term>Liaison aux protéines</term><term>Régions 5' non traduites (génétique)</term><term>Régions promotrices (génétique) (génétique)</term><term>Régulation de l'expression des gènes</term><term>Site d'initiation de la transcription</term><term>Sites de fixation</term><term>Séquence nucléotidique</term><term>Transcription génétique (génétique)</term><term>Éléments de réponse (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>5' Untranslated Regions</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Promoter Regions, Genetic</term><term>Response Elements</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Régions 5' non traduites</term><term>Régions promotrices (génétique)</term><term>Transcription génétique</term><term>Éléments de réponse</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Computational Biology</term><term>Databases, Genetic</term><term>Gene Expression Regulation</term><term>Humans</term><term>Molecular Sequence Data</term><term>Protein Binding</term><term>Transcription Initiation Site</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Liaison aux protéines</term><term>Régulation de l'expression des gènes</term><term>Site d'initiation de la transcription</term><term>Sites de fixation</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Central to reconstruction of cis-regulatory networks is identification and classification of naturally occurring transcription factor-binding sites according to the genes that they control. We have examined salient characteristics of 9-mers that occur in various orders and combinations in the proximal promoters of human genes. In evaluations of a dataset derived with respect to experimentally defined transcription initiation sites, in some cases we observed a clear correspondence of highly ranked 9-mers with protein-binding sites in genomic DNA. Evaluations of the larger dataset, derived with respect to the 5' end of human ESTs, revealed that a subset of the highly ranked 9-mers corresponded to sites for several known transcription factor families (including CREB, ETS, EGR-1, SP1, KLF, MAZ, HIF-1, and STATs) that play important roles in the regulation of vertebrate genes. We identified several highly ranked CpG-containing 9-mers, defining sites for interactions with the CREB and ETS families of proteins, and identified potential target genes for these proteins. The results of the studies imply that the CpG-containing transcription factor-binding sites regulate the expression of genes with important roles in pathways leading to cell-type-specific gene expression and pathways controlled by the complex networks of signaling systems.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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