Exploring transcription factor binding properties of several non-coding DNA sequence elements in the human NF-IL6 gene.
Identifieur interne : 002D29 ( Main/Exploration ); précédent : 002D28; suivant : 002D30Exploring transcription factor binding properties of several non-coding DNA sequence elements in the human NF-IL6 gene.
Auteurs : Elsie I. Pares-Matos [États-Unis] ; Jason S. Milligan ; Minou BinaSource :
- Journal of molecular biology [ 0022-2836 ] ; 2006.
Descripteurs français
- KwdFr :
- ADN (métabolisme), Animaux, Cellules U937, Données de séquences moléculaires, Humains, Liaison aux protéines (génétique), Pan troglodytes, Poulets, Protéine bêta de liaison aux séquences stimulatrices de type CCAAT (génétique), Protéine bêta de liaison aux séquences stimulatrices de type CCAAT (métabolisme), Protéine bêta de liaison aux séquences stimulatrices de type CCAAT (physiologie), Rats, Souris, Séquence conservée (génétique), Séquence nucléotidique, Séquence riche en GC, Test de retard de migration électrophorétique, Transduction du signal (génétique), Éléments de régulation transcriptionnelle (physiologie).
- MESH :
- génétique : Liaison aux protéines, Protéine bêta de liaison aux séquences stimulatrices de type CCAAT, Séquence conservée, Transduction du signal.
- métabolisme : ADN, Protéine bêta de liaison aux séquences stimulatrices de type CCAAT.
- physiologie : Protéine bêta de liaison aux séquences stimulatrices de type CCAAT, Éléments de régulation transcriptionnelle.
- Animaux, Cellules U937, Données de séquences moléculaires, Humains, Pan troglodytes, Poulets, Rats, Souris, Séquence nucléotidique, Séquence riche en GC, Test de retard de migration électrophorétique.
English descriptors
- KwdEn :
- Animals, Base Sequence, CCAAT-Enhancer-Binding Protein-beta (genetics), CCAAT-Enhancer-Binding Protein-beta (metabolism), CCAAT-Enhancer-Binding Protein-beta (physiology), Chickens, Conserved Sequence (genetics), DNA (metabolism), Electrophoretic Mobility Shift Assay, GC Rich Sequence, Humans, Mice, Molecular Sequence Data, Pan troglodytes, Protein Binding (genetics), Rats, Regulatory Elements, Transcriptional (physiology), Signal Transduction (genetics), U937 Cells.
- MESH :
- chemical , genetics : CCAAT-Enhancer-Binding Protein-beta.
- chemical , metabolism : CCAAT-Enhancer-Binding Protein-beta, DNA.
- chemical , physiology : CCAAT-Enhancer-Binding Protein-beta.
- genetics : Conserved Sequence, Protein Binding, Signal Transduction.
- physiology : Regulatory Elements, Transcriptional.
- Animals, Base Sequence, Chickens, Electrophoretic Mobility Shift Assay, GC Rich Sequence, Humans, Mice, Molecular Sequence Data, Pan troglodytes, Rats, U937 Cells.
Abstract
We examined several DNA segments upstream of the transcription start site of the human NF-IL6 gene to evaluate the predictions of two computational models developed to identify potential regulatory elements in the non-coding regions of genes. One model, comparative genomics, is based on the hypothesis that functional regulatory sequences can be localized in alignments of genomic DNA from several species. The other model is based on the hypothesis that protein-binding sites in genomic DNA may include sequence elements that occur frequently in proximal promoters of genes. The segments selected for DNA binding and functional evaluations included: (1) two conserved regions identified in multi-species sequence alignments; (2) a region containing several localized hits with 9-mers that ranked highly in studies of proximal promoters of human genes; and (3) two regions that were either GC-rich and/or contained tracts of G. The assays were done under nearly identical experimental conditions, using a cell line (U937) representing human monocytes/macrophages. The experiments also aimed at evaluating what effect, if any, cellular stimulation could have on the interactions of nuclear proteins with naturally occurring GC-rich elements in a human genomic DNA. In DNA binding assays, several complexes were formed with the conserved regions identified in multi-species sequence alignment. Furthermore, these regions were active in functional assays. The region containing several matches with 9-mers derived from proximal promoters of human genes was not conserved but formed several complexes with nuclear proteins including Sp1, Egr-1, and an unidentified protein. In addition, this region was active in functional assays and responded to cellular stimulations. Overall, the results of the assays suggest an important role for the sequence context of genomic DNA in protein binding and selection.
DOI: 10.1016/j.jmb.2005.12.071
PubMed: 16458921
Affiliations:
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Pares-Matos</name><affiliation wicri:level="2"><nlm:affiliation>Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Purdue University, West Lafayette, IN 47907</wicri:regionArea><placeName><region type="state">Indiana</region></placeName></affiliation></author><author><name sortKey="Milligan, Jason S" sort="Milligan, Jason S" uniqKey="Milligan J" first="Jason S" last="Milligan">Jason S. Milligan</name></author><author><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>CCAAT-Enhancer-Binding Protein-beta (genetics)</term><term>CCAAT-Enhancer-Binding Protein-beta (metabolism)</term><term>CCAAT-Enhancer-Binding Protein-beta (physiology)</term><term>Chickens</term><term>Conserved Sequence (genetics)</term><term>DNA (metabolism)</term><term>Electrophoretic Mobility Shift Assay</term><term>GC Rich Sequence</term><term>Humans</term><term>Mice</term><term>Molecular Sequence Data</term><term>Pan troglodytes</term><term>Protein Binding (genetics)</term><term>Rats</term><term>Regulatory Elements, Transcriptional (physiology)</term><term>Signal Transduction (genetics)</term><term>U937 Cells</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (métabolisme)</term><term>Animaux</term><term>Cellules U937</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Liaison aux protéines (génétique)</term><term>Pan troglodytes</term><term>Poulets</term><term>Protéine bêta de liaison aux séquences stimulatrices de type CCAAT (génétique)</term><term>Protéine bêta de liaison aux séquences stimulatrices de type CCAAT (métabolisme)</term><term>Protéine bêta de liaison aux séquences stimulatrices de type CCAAT (physiologie)</term><term>Rats</term><term>Souris</term><term>Séquence conservée (génétique)</term><term>Séquence nucléotidique</term><term>Séquence riche en GC</term><term>Test de retard de migration électrophorétique</term><term>Transduction du signal (génétique)</term><term>Éléments de régulation transcriptionnelle (physiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>CCAAT-Enhancer-Binding Protein-beta</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>CCAAT-Enhancer-Binding Protein-beta</term><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en"><term>CCAAT-Enhancer-Binding Protein-beta</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Conserved Sequence</term><term>Protein Binding</term><term>Signal Transduction</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Liaison aux protéines</term><term>Protéine bêta de liaison aux séquences stimulatrices de type CCAAT</term><term>Séquence conservée</term><term>Transduction du signal</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Protéine bêta de liaison aux séquences stimulatrices de type CCAAT</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Protéine bêta de liaison aux séquences stimulatrices de type CCAAT</term><term>Éléments de régulation transcriptionnelle</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Regulatory Elements, Transcriptional</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Chickens</term><term>Electrophoretic Mobility Shift Assay</term><term>GC Rich Sequence</term><term>Humans</term><term>Mice</term><term>Molecular Sequence Data</term><term>Pan troglodytes</term><term>Rats</term><term>U937 Cells</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Cellules U937</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Pan troglodytes</term><term>Poulets</term><term>Rats</term><term>Souris</term><term>Séquence nucléotidique</term><term>Séquence riche en GC</term><term>Test de retard de migration électrophorétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We examined several DNA segments upstream of the transcription start site of the human NF-IL6 gene to evaluate the predictions of two computational models developed to identify potential regulatory elements in the non-coding regions of genes. One model, comparative genomics, is based on the hypothesis that functional regulatory sequences can be localized in alignments of genomic DNA from several species. The other model is based on the hypothesis that protein-binding sites in genomic DNA may include sequence elements that occur frequently in proximal promoters of genes. The segments selected for DNA binding and functional evaluations included: (1) two conserved regions identified in multi-species sequence alignments; (2) a region containing several localized hits with 9-mers that ranked highly in studies of proximal promoters of human genes; and (3) two regions that were either GC-rich and/or contained tracts of G. The assays were done under nearly identical experimental conditions, using a cell line (U937) representing human monocytes/macrophages. The experiments also aimed at evaluating what effect, if any, cellular stimulation could have on the interactions of nuclear proteins with naturally occurring GC-rich elements in a human genomic DNA. In DNA binding assays, several complexes were formed with the conserved regions identified in multi-species sequence alignment. Furthermore, these regions were active in functional assays. The region containing several matches with 9-mers derived from proximal promoters of human genes was not conserved but formed several complexes with nuclear proteins including Sp1, Egr-1, and an unidentified protein. In addition, this region was active in functional assays and responded to cellular stimulations. Overall, the results of the assays suggest an important role for the sequence context of genomic DNA in protein binding and selection.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Indiana</li></region></list><tree><noCountry><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name><name sortKey="Milligan, Jason S" sort="Milligan, Jason S" uniqKey="Milligan J" first="Jason S" last="Milligan">Jason S. Milligan</name></noCountry><country name="États-Unis"><region name="Indiana"><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></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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