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A genome scale location analysis of hStaf/ZNF143 binding sites suggest a widespread role for hStaf/ZNF143 in the mammalian promoters
Staf was originally identified as the transcriptional activator of Xenopus tRNASec and snRNA-type genes. Recently, transcription of seven human protein coding genes was reported to be activated by the human ortholog hStaf/ZNF143. Here, we have used a combined in silico and biochemical approach to id...
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Published in: | The Journal of biological chemistry 2006-11 |
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creator | Myslinski, Evelyne Gérard, Marie-Aline Krol, Alain Carbon, Philippe |
description | Staf was originally identified as the transcriptional activator of Xenopus tRNASec and snRNA-type genes. Recently, transcription of seven human protein coding genes was reported to be activated by the human ortholog hStaf/ZNF143. Here, we have used a combined in silico and biochemical approach to identify 1175 conserved hStaf/ZNF143 binding sites (SBS) distributed in 938 promoters of four mammalian genomes. The SBS shows a significant positional preference and occurs mostly within 200 bp upstream of the transcription start site. Chromatin immunoprecipitation assays with 295 of the promoters established that 90% contain bona fide SBS. By extrapolating the values of this mapping to the full sizes of the mammalian genomes, we can infer the existence of at least 2500 SBS distributed in 2000 promoters. This unexpected large number strongly suggests that SBS constitutes one of the most widespread transcription factor binding sites in mammalian promoters. Furthermore, we demonstrated that the presence of the SBS alone is sufficient to direct expression of a luciferase reporter gene, suggesting that hStaf/ZNF143 can recruit per se the transcription machinery. |
doi_str_mv | 10.1074/jbc.M608507200 |
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Recently, transcription of seven human protein coding genes was reported to be activated by the human ortholog hStaf/ZNF143. Here, we have used a combined in silico and biochemical approach to identify 1175 conserved hStaf/ZNF143 binding sites (SBS) distributed in 938 promoters of four mammalian genomes. The SBS shows a significant positional preference and occurs mostly within 200 bp upstream of the transcription start site. Chromatin immunoprecipitation assays with 295 of the promoters established that 90% contain bona fide SBS. By extrapolating the values of this mapping to the full sizes of the mammalian genomes, we can infer the existence of at least 2500 SBS distributed in 2000 promoters. This unexpected large number strongly suggests that SBS constitutes one of the most widespread transcription factor binding sites in mammalian promoters. Furthermore, we demonstrated that the presence of the SBS alone is sufficient to direct expression of a luciferase reporter gene, suggesting that hStaf/ZNF143 can recruit per se the transcription machinery.</description><identifier>ISSN: 0021-9258</identifier><identifier>EISSN: 1083-351X</identifier><identifier>DOI: 10.1074/jbc.M608507200</identifier><identifier>PMID: 17092945</identifier><language>eng</language><publisher>American Society for Biochemistry and Molecular Biology</publisher><subject>Cellular Biology ; Life Sciences</subject><ispartof>The Journal of biological chemistry, 2006-11</ispartof><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27923,27924</link.rule.ids><backlink>$$Uhttps://hal.science/hal-00120109$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Myslinski, Evelyne</creatorcontrib><creatorcontrib>Gérard, Marie-Aline</creatorcontrib><creatorcontrib>Krol, Alain</creatorcontrib><creatorcontrib>Carbon, Philippe</creatorcontrib><title>A genome scale location analysis of hStaf/ZNF143 binding sites suggest a widespread role for hStaf/ZNF143 in the mammalian promoters</title><title>The Journal of biological chemistry</title><description>Staf was originally identified as the transcriptional activator of Xenopus tRNASec and snRNA-type genes. Recently, transcription of seven human protein coding genes was reported to be activated by the human ortholog hStaf/ZNF143. Here, we have used a combined in silico and biochemical approach to identify 1175 conserved hStaf/ZNF143 binding sites (SBS) distributed in 938 promoters of four mammalian genomes. The SBS shows a significant positional preference and occurs mostly within 200 bp upstream of the transcription start site. Chromatin immunoprecipitation assays with 295 of the promoters established that 90% contain bona fide SBS. By extrapolating the values of this mapping to the full sizes of the mammalian genomes, we can infer the existence of at least 2500 SBS distributed in 2000 promoters. This unexpected large number strongly suggests that SBS constitutes one of the most widespread transcription factor binding sites in mammalian promoters. 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Recently, transcription of seven human protein coding genes was reported to be activated by the human ortholog hStaf/ZNF143. Here, we have used a combined in silico and biochemical approach to identify 1175 conserved hStaf/ZNF143 binding sites (SBS) distributed in 938 promoters of four mammalian genomes. The SBS shows a significant positional preference and occurs mostly within 200 bp upstream of the transcription start site. Chromatin immunoprecipitation assays with 295 of the promoters established that 90% contain bona fide SBS. By extrapolating the values of this mapping to the full sizes of the mammalian genomes, we can infer the existence of at least 2500 SBS distributed in 2000 promoters. This unexpected large number strongly suggests that SBS constitutes one of the most widespread transcription factor binding sites in mammalian promoters. Furthermore, we demonstrated that the presence of the SBS alone is sufficient to direct expression of a luciferase reporter gene, suggesting that hStaf/ZNF143 can recruit per se the transcription machinery.</abstract><pub>American Society for Biochemistry and Molecular Biology</pub><pmid>17092945</pmid><doi>10.1074/jbc.M608507200</doi></addata></record> |
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title | A genome scale location analysis of hStaf/ZNF143 binding sites suggest a widespread role for hStaf/ZNF143 in the mammalian promoters |
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