Determination of the human c-Abl consensus DNA binding site
Identifieur interne : 001059 ( Istex/Corpus ); précédent : 001058; suivant : 001060Determination of the human c-Abl consensus DNA binding site
Auteurs : Marie-Hélène David-Cordonnier ; Malika Hamdane ; Christian Bailly ; Jean-Claude D'HalluinSource :
- FEBS Letters [ 0014-5793 ] ; 1998.
English descriptors
- Teeft :
- Actin binding site, Anking sequences, Base pairs, Binding activity, Binding capacity, Binding domain, Binding sites, Bold letters, Cell cycle, Clone, Computer programs, Consensus binding site, Consensus sequence, Deletion, Deletion mutants, Dnase, Domain, Feb, Fusion peptide, Fusion protein, Human protein, Kinase, Klenow enzyme, Large domain, Ligue nationale contre, Lille, Mouse protein, Mutant, Protein binding site, Secondary structure, Target site, Threonine residues, Tyrosine, Tyrosine kinase, Wang.
Abstract
Abstract: c-Abl tyrosine kinase, an essential protein of the cell cycle signalling pathways, is implicated in the regulation of RNA polymerase II activity, apoptosis and DNA repair. Its DNA binding activity is important for its biological functions. However, the molecular basis of c-Abl interaction with DNA remains largely unclear. We delimited the human c-Abl DNA binding domain and identified its preferred binding site, 5′-AA/CAACAAA/C. The central AAC motif is highly conserved and constitutes the major core element in the binding sites. EMSAs and footprinting experiments were performed to explore how the c-Abl fusion protein recognizes specific sequences in DNA.
Url:
DOI: 10.1016/S0014-5793(98)00169-0
Links to Exploration step
ISTEX:DF35ED7E47178F4D89B17D09642A0B6C8CE8266DLe document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>Determination of the human c-Abl consensus DNA binding site</title><author><name sortKey="David Cordonnier, Marie Helene" sort="David Cordonnier, Marie Helene" uniqKey="David Cordonnier M" first="Marie-Hélène" last="David-Cordonnier">Marie-Hélène David-Cordonnier</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation></author><author><name sortKey="Hamdane, Malika" sort="Hamdane, Malika" uniqKey="Hamdane M" first="Malika" last="Hamdane">Malika Hamdane</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation></author><author><name sortKey="Bailly, Christian" sort="Bailly, Christian" uniqKey="Bailly C" first="Christian" last="Bailly">Christian Bailly</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation></author><author><name sortKey="D Halluin, Jean Claude" sort="D Halluin, Jean Claude" uniqKey="D Halluin J" first="Jean-Claude" last="D'Halluin">Jean-Claude D'Halluin</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Corresponding author. Fax: (33) 3 20 16 92 29. E-mail: jcd@lille.inserm.fr</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:DF35ED7E47178F4D89B17D09642A0B6C8CE8266D</idno><date when="1998" year="1998">1998</date><idno type="doi">10.1016/S0014-5793(98)00169-0</idno><idno type="url">https://api.istex.fr/ark:/67375/6H6-10DVCWBB-T/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001059</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001059</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a">Determination of the human c-Abl consensus DNA binding site</title><author><name sortKey="David Cordonnier, Marie Helene" sort="David Cordonnier, Marie Helene" uniqKey="David Cordonnier M" first="Marie-Hélène" last="David-Cordonnier">Marie-Hélène David-Cordonnier</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation></author><author><name sortKey="Hamdane, Malika" sort="Hamdane, Malika" uniqKey="Hamdane M" first="Malika" last="Hamdane">Malika Hamdane</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation></author><author><name sortKey="Bailly, Christian" sort="Bailly, Christian" uniqKey="Bailly C" first="Christian" last="Bailly">Christian Bailly</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation></author><author><name sortKey="D Halluin, Jean Claude" sort="D Halluin, Jean Claude" uniqKey="D Halluin J" first="Jean-Claude" last="D'Halluin">Jean-Claude D'Halluin</name><affiliation><mods:affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</mods:affiliation></affiliation><affiliation><mods:affiliation>Corresponding author. Fax: (33) 3 20 16 92 29. E-mail: jcd@lille.inserm.fr</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">FEBS Letters</title><title level="j" type="abbrev">FEBS</title><idno type="ISSN">0014-5793</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1998">1998</date><biblScope unit="volume">424</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="177">177</biblScope><biblScope unit="page" to="182">182</biblScope></imprint><idno type="ISSN">0014-5793</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0014-5793</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Actin binding site</term><term>Anking sequences</term><term>Base pairs</term><term>Binding activity</term><term>Binding capacity</term><term>Binding domain</term><term>Binding sites</term><term>Bold letters</term><term>Cell cycle</term><term>Clone</term><term>Computer programs</term><term>Consensus binding site</term><term>Consensus sequence</term><term>Deletion</term><term>Deletion mutants</term><term>Dnase</term><term>Domain</term><term>Feb</term><term>Fusion peptide</term><term>Fusion protein</term><term>Human protein</term><term>Kinase</term><term>Klenow enzyme</term><term>Large domain</term><term>Ligue nationale contre</term><term>Lille</term><term>Mouse protein</term><term>Mutant</term><term>Protein binding site</term><term>Secondary structure</term><term>Target site</term><term>Threonine residues</term><term>Tyrosine</term><term>Tyrosine kinase</term><term>Wang</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: c-Abl tyrosine kinase, an essential protein of the cell cycle signalling pathways, is implicated in the regulation of RNA polymerase II activity, apoptosis and DNA repair. Its DNA binding activity is important for its biological functions. However, the molecular basis of c-Abl interaction with DNA remains largely unclear. We delimited the human c-Abl DNA binding domain and identified its preferred binding site, 5′-AA/CAACAAA/C. The central AAC motif is highly conserved and constitutes the major core element in the binding sites. 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Fax: (33) 3 20 16 92 29. E-mail: jcd@lille.inserm.fr</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>CASTing</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DNA binding</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Tyrosine kinase</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Transcription factor</value></json:item></subject><arkIstex>ark:/67375/6H6-10DVCWBB-T</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: c-Abl tyrosine kinase, an essential protein of the cell cycle signalling pathways, is implicated in the regulation of RNA polymerase II activity, apoptosis and DNA repair. Its DNA binding activity is important for its biological functions. However, the molecular basis of c-Abl interaction with DNA remains largely unclear. We delimited the human c-Abl DNA binding domain and identified its preferred binding site, 5′-AA/CAACAAA/C. The central AAC motif is highly conserved and constitutes the major core element in the binding sites. EMSAs and footprinting experiments were performed to explore how the c-Abl fusion protein recognizes specific sequences in DNA.</abstract><qualityIndicators><score>6.844</score><pdfWordCount>3656</pdfWordCount><pdfCharCount>20845</pdfCharCount><pdfVersion>1.2</pdfVersion><pdfPageCount>6</pdfPageCount><pdfPageSize>588 x 804 pts</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>99</abstractWordCount><abstractCharCount>672</abstractCharCount><keywordCount>4</keywordCount></qualityIndicators><title>Determination of the human c-Abl consensus DNA binding site</title><pmid><json:string>9539146</json:string></pmid><pii><json:string>S0014-5793(98)00169-0</json:string></pii><genre><json:string>research-article</json:string></genre><host><title>FEBS Letters</title><language><json:string>unknown</json:string></language><publicationDate>1998</publicationDate><issn><json:string>0014-5793</json:string></issn><pii><json:string>S0014-5793(00)X0158-5</json:string></pii><volume>424</volume><issue>3</issue><pages><first>177</first><last>182</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>1998</json:string></date><geogName></geogName><orgName></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>G. 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David-Cordonnier et al.</json:string><json:string>[5]</json:string><json:string>[15]</json:string><json:string>[30]</json:string><json:string>[25]</json:string><json:string>[1,2]</json:string><json:string>[19]</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-10DVCWBB-T</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - cell biology</json:string><json:string>2 - biophysics</json:string><json:string>2 - biochemistry & molecular biology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - biochemistry & molecular biology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Cell Biology</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Genetics</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Molecular Biology</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Biochemistry</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Structural Biology</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Biophysics</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>1998</publicationDate><copyrightDate>1998</copyrightDate><doi><json:string>10.1016/S0014-5793(98)00169-0</json:string></doi><id>DF35ED7E47178F4D89B17D09642A0B6C8CE8266D</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-10DVCWBB-T/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-10DVCWBB-T/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-10DVCWBB-T/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a">Determination of the human c-Abl consensus DNA binding site</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>©1998 Federation of European Biochemical Societies</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</p></availability><date>1998</date></publicationStmt><notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note><note type="content">Fig. 1: Binding of c-Abl deletion mutants to DNA-cellulose. The deletion and fusion proteins were prepared with the indicated restriction enzymes. The relative affinity of the deletion mutants is given with respect to that of the BB protein used as a control (eluted with 300 mM NaCl). Symbols +++ and ++ indicate that the DNA binding capacity is equivalent and slightly reduced compared to that of the BB protein, respectively. The symbol ± denotes weak binding capacity. The double deletion mutant BBΔSma-ΔPst binds to the DNA-cellulose only at low stringency (100 mM NaCl).</note><note type="content">Fig. 2: Potential secondary structure of the NX-HIS fusion peptide. The computer programs GSM, Garnier, Gibrat, Levin, DPM, and SOPMA were used to determine the position of the α-helices, β-sheets or coiled structures within the DNA binding domain of c-Abl (fragment corresponding to the NX protein). The consensus sequence was derived from the complementary computer analyses. H, E, C and T represent α-helix, β-sheet, coil and turn conformations, respectively.</note><note type="content">Fig. 3: The oligonucleotides 01–40 were sequenced after nine rounds of selection-amplification for c-Abl DNA binding ability. The upper sequences are aligned to show the sequence homology and were used to determine the consensus shown in bold letters.</note><note type="content">Fig. 4: EMSA showing the binding of the DNA binding domain of c-Abl to the XbaI-XhoI fragments containing the selected 01, 02, 03, 05, 10, 17 or the control SK sequences. The duplex oligonucleotide was incubated with (+) or without (−) 1 μM of GST-NX-HIS in the presence of a 500-fold molar excess of poly(dI-dC)·(dI-dC). The SK probe containing the pBSIISK plasmid sequence but lacking the protein binding site was used as a control.</note><note type="content">Fig. 5: DNase I footprinting of the GST-NX-HIS protein on the XbaI-XhoI fragment of clone 05. The 73 bp DNA fragment was 3′ end-labelled at the XbaI site. The GST-NX-HIS fusion protein (lane GNX) or BSA in the control (lane C) (10 μM each) was incubated with the DNA for 15 min at 30°C before digestion with 0.05 units of DNase I. The products of the DNase I digestion were identified by reference to the guanine markers (lane G). A portion of the DNA sequence is indicated on the side of the gel. The sequence protected from DNase I cleavage is bracketed and the sequence of oligonucleotide 05 that binds to the protein is shown in bold letters.</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a">Determination of the human c-Abl consensus DNA binding site</title><author xml:id="author-0000"><persName><forename type="first">Marie-Hélène</forename><surname>David-Cordonnier</surname></persName><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation></author><author xml:id="author-0001"><persName><forename type="first">Malika</forename><surname>Hamdane</surname></persName><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation></author><author xml:id="author-0002"><persName><forename type="first">Christian</forename><surname>Bailly</surname></persName><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation><affiliation>Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation></author><author xml:id="author-0003"><persName><forename type="first">Jean-Claude</forename><surname>D'Halluin</surname></persName><email>jcd@lille.inserm.fr</email><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation></author><idno type="istex">DF35ED7E47178F4D89B17D09642A0B6C8CE8266D</idno><idno type="ark">ark:/67375/6H6-10DVCWBB-T</idno><idno type="DOI">10.1016/S0014-5793(98)00169-0</idno><idno type="PII">S0014-5793(98)00169-0</idno></analytic><monogr><title level="j">FEBS Letters</title><title level="j" type="abbrev">FEBS</title><idno type="pISSN">0014-5793</idno><idno type="PII">S0014-5793(00)X0158-5</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1998"></date><biblScope unit="volume">424</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="177">177</biblScope><biblScope unit="page" to="182">182</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>1998</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: c-Abl tyrosine kinase, an essential protein of the cell cycle signalling pathways, is implicated in the regulation of RNA polymerase II activity, apoptosis and DNA repair. Its DNA binding activity is important for its biological functions. However, the molecular basis of c-Abl interaction with DNA remains largely unclear. We delimited the human c-Abl DNA binding domain and identified its preferred binding site, 5′-AA/CAACAAA/C. The central AAC motif is highly conserved and constitutes the major core element in the binding sites. EMSAs and footprinting experiments were performed to explore how the c-Abl fusion protein recognizes specific sequences in DNA.</p></abstract><textClass><keywords scheme="keyword"><list><head>Keywords</head><item><term>CASTing</term></item><item><term>DNA binding</term></item><item><term>Tyrosine kinase</term></item><item><term>Transcription factor</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1998">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-10DVCWBB-T/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: ce:floats; body; tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"><istex:entity SYSTEM="gr1" NDATA="IMAGE" name="gr1"></istex:entity><istex:entity SYSTEM="gr2" NDATA="IMAGE" name="gr2"></istex:entity><istex:entity SYSTEM="gr3" NDATA="IMAGE" name="gr3"></istex:entity><istex:entity SYSTEM="gr4" NDATA="IMAGE" name="gr4"></istex:entity><istex:entity SYSTEM="gr5" NDATA="IMAGE" name="gr5"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla"><item-info><jid>FEBS</jid><aid>19936</aid><ce:pii>S0014-5793(98)00169-0</ce:pii><ce:doi>10.1016/S0014-5793(98)00169-0</ce:doi><ce:copyright year="1998" type="society">Federation of European Biochemical Societies</ce:copyright></item-info><head><ce:title>Determination of the human c-Abl consensus DNA binding site</ce:title><ce:author-group><ce:author><ce:given-name>Marie-Hélène</ce:given-name><ce:surname>David-Cordonnier</ce:surname><ce:cross-ref refid="AFF1">a</ce:cross-ref></ce:author><ce:author><ce:given-name>Malika</ce:given-name><ce:surname>Hamdane</ce:surname><ce:cross-ref refid="AFF1">a</ce:cross-ref></ce:author><ce:author><ce:given-name>Christian</ce:given-name><ce:surname>Bailly</ce:surname><ce:cross-ref refid="AFF1">a</ce:cross-ref><ce:cross-ref refid="AFF2">b</ce:cross-ref></ce:author><ce:author><ce:given-name>Jean-Claude</ce:given-name><ce:surname>D'Halluin</ce:surname><ce:cross-ref refid="AFF1">a</ce:cross-ref><ce:cross-ref refid="CORR1">*</ce:cross-ref></ce:author><ce:affiliation id="AFF1"><ce:label>a</ce:label><ce:textfn>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</ce:textfn></ce:affiliation><ce:affiliation id="AFF2"><ce:label>b</ce:label><ce:textfn>Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</ce:textfn></ce:affiliation><ce:correspondence id="CORR1"><ce:label>*</ce:label><ce:text>Corresponding author. Fax: (33) 3 20 16 92 29. E-mail: jcd@lille.inserm.fr</ce:text></ce:correspondence></ce:author-group><ce:date-received day="3" month="12" year="1997"></ce:date-received><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>c-Abl tyrosine kinase, an essential protein of the cell cycle signalling pathways, is implicated in the regulation of RNA polymerase II activity, apoptosis and DNA repair. Its DNA binding activity is important for its biological functions. However, the molecular basis of c-Abl interaction with DNA remains largely unclear. We delimited the human c-Abl DNA binding domain and identified its preferred binding site, 5′-A<ce:sup>A</ce:sup>/<ce:inf>C</ce:inf>AACAA<ce:sup>A</ce:sup>/<ce:inf>C</ce:inf>. The central AAC motif is highly conserved and constitutes the major core element in the binding sites. EMSAs and footprinting experiments were performed to explore how the c-Abl fusion protein recognizes specific sequences in DNA.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords class="keyword"><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>CASTing</ce:text></ce:keyword><ce:keyword><ce:text>DNA binding</ce:text></ce:keyword><ce:keyword><ce:text>Tyrosine kinase</ce:text></ce:keyword><ce:keyword><ce:text>Transcription factor</ce:text></ce:keyword></ce:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Determination of the human c-Abl consensus DNA binding site</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Determination of the human c-Abl consensus DNA binding site</title></titleInfo><name type="personal"><namePart type="given">Marie-Hélène</namePart><namePart type="family">David-Cordonnier</namePart><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Malika</namePart><namePart type="family">Hamdane</namePart><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Christian</namePart><namePart type="family">Bailly</namePart><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation><affiliation>Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jean-Claude</namePart><namePart type="family">D'Halluin</namePart><affiliation>INSERM U 124 Onco-hématologie moléculaire, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille, France</affiliation><affiliation>Corresponding author. Fax: (33) 3 20 16 92 29. E-mail: jcd@lille.inserm.fr</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1998</dateIssued><copyrightDate encoding="w3cdtf">1998</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Abstract: c-Abl tyrosine kinase, an essential protein of the cell cycle signalling pathways, is implicated in the regulation of RNA polymerase II activity, apoptosis and DNA repair. Its DNA binding activity is important for its biological functions. However, the molecular basis of c-Abl interaction with DNA remains largely unclear. We delimited the human c-Abl DNA binding domain and identified its preferred binding site, 5′-AA/CAACAAA/C. The central AAC motif is highly conserved and constitutes the major core element in the binding sites. EMSAs and footprinting experiments were performed to explore how the c-Abl fusion protein recognizes specific sequences in DNA.</abstract><note type="content">Fig. 1: Binding of c-Abl deletion mutants to DNA-cellulose. The deletion and fusion proteins were prepared with the indicated restriction enzymes. The relative affinity of the deletion mutants is given with respect to that of the BB protein used as a control (eluted with 300 mM NaCl). Symbols +++ and ++ indicate that the DNA binding capacity is equivalent and slightly reduced compared to that of the BB protein, respectively. The symbol ± denotes weak binding capacity. The double deletion mutant BBΔSma-ΔPst binds to the DNA-cellulose only at low stringency (100 mM NaCl).</note><note type="content">Fig. 2: Potential secondary structure of the NX-HIS fusion peptide. The computer programs GSM, Garnier, Gibrat, Levin, DPM, and SOPMA were used to determine the position of the α-helices, β-sheets or coiled structures within the DNA binding domain of c-Abl (fragment corresponding to the NX protein). The consensus sequence was derived from the complementary computer analyses. H, E, C and T represent α-helix, β-sheet, coil and turn conformations, respectively.</note><note type="content">Fig. 3: The oligonucleotides 01–40 were sequenced after nine rounds of selection-amplification for c-Abl DNA binding ability. The upper sequences are aligned to show the sequence homology and were used to determine the consensus shown in bold letters.</note><note type="content">Fig. 4: EMSA showing the binding of the DNA binding domain of c-Abl to the XbaI-XhoI fragments containing the selected 01, 02, 03, 05, 10, 17 or the control SK sequences. The duplex oligonucleotide was incubated with (+) or without (−) 1 μM of GST-NX-HIS in the presence of a 500-fold molar excess of poly(dI-dC)·(dI-dC). The SK probe containing the pBSIISK plasmid sequence but lacking the protein binding site was used as a control.</note><note type="content">Fig. 5: DNase I footprinting of the GST-NX-HIS protein on the XbaI-XhoI fragment of clone 05. The 73 bp DNA fragment was 3′ end-labelled at the XbaI site. The GST-NX-HIS fusion protein (lane GNX) or BSA in the control (lane C) (10 μM each) was incubated with the DNA for 15 min at 30°C before digestion with 0.05 units of DNase I. The products of the DNase I digestion were identified by reference to the guanine markers (lane G). A portion of the DNA sequence is indicated on the side of the gel. The sequence protected from DNase I cleavage is bracketed and the sequence of oligonucleotide 05 that binds to the protein is shown in bold letters.</note><subject><genre>Keywords</genre><topic>CASTing</topic><topic>DNA binding</topic><topic>Tyrosine kinase</topic><topic>Transcription factor</topic></subject><relatedItem type="host"><titleInfo><title>FEBS Letters</title></titleInfo><titleInfo type="abbreviated"><title>FEBS</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1998</dateIssued></originInfo><identifier type="ISSN">0014-5793</identifier><identifier type="PII">S0014-5793(00)X0158-5</identifier><part><date>1998</date><detail type="volume"><number>424</number><caption>vol.</caption></detail><detail type="issue"><number>3</number><caption>no.</caption></detail><extent unit="issue-pages"><start>121</start><end>290</end></extent><extent unit="pages"><start>177</start><end>182</end></extent></part></relatedItem><identifier type="istex">DF35ED7E47178F4D89B17D09642A0B6C8CE8266D</identifier><identifier type="ark">ark:/67375/6H6-10DVCWBB-T</identifier><identifier type="DOI">10.1016/S0014-5793(98)00169-0</identifier><identifier type="PII">S0014-5793(98)00169-0</identifier><accessCondition type="use and reproduction" contentType="copyright">©1998 Federation of European Biochemical Societies</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</recordContentSource><recordOrigin>Federation of European Biochemical Societies, ©1998</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-10DVCWBB-T/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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