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Keywords {🔍}

factors, bound, regions, pubmed, data, google, scholar, binding, drosophila, factor, transcription, figure, gene, file, genes, additional, highly, chipchip, fdr, dna, crms, peak, genome, peaks, genomic, shown, scores, expression, development, early, blastoderm, regulatory, analysis, central, overlap, embryos, protein, regulators, vivo, proteins, targets, table, cohorts, sequences, embryo, region, antibodies, dev, quantitative, pair,

Topics {✒️}

energy contract de-ac02-05ch11231 false discovery rate mann-whitney tests applied cis-acting control elements transcriptional regulatory networks eurographics/ieee-vgtc symposium sequence-specific transcription factors genomic regulatory networks gov/fly-net/chipchip gov/fly-net/bioimaging chip-chip rank list chip/chip rank list mann-whitney test vertebrate-encoded transcription factors pair-rule gene runt gene ontology consortium false negative rate article number r80 sox-domain protein required article download pdf multiple promoter elements oligo chip/chip scores initiate anterior/posterior patterning post-dna-binding events extended cis-regulatory region 500-bp chip/chip peaks earlier southern blot-based stripe pair-rule pattern chip/chip peak scores performed chip/chip experiments chip/chip peaks shows related subjects genome chip-chip analysis sequence-specific factors luengo hendriks cl transcription factor access transcriptional regulatory activities homeoprotein-dna binding sites public web site network controlling transcription core transcriptional network hundred base-pair segment degenerate dna sequences o'farrell ph e2f1-binding sites suggests cis-regulatory modules privacy choices/manage cookies yeast pho5 promoter bonferonni corrected values vivo protein-dna interactions

Questions {❓}

• How is it possible to have so much binding that has no or little effect on transcription?
• What mechanism, though, drives the extraordinarily extensive, overlapping pattern of binding?

Schema {🗺️}

WebPage:
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         headline:Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
         description:We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.
         datePublished:2009-07-23T00:00:00Z
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            False Discovery Rate
            Additional Data File
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            Regulatory Classis
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
      description:We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.
      datePublished:2009-07-23T00:00:00Z
      dateModified:2009-07-23T00:00:00Z
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      pageEnd:26
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         Gene Ontology
         False Discovery Rate
         Additional Data File
         Functional Target
         Regulatory Classis
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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         name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
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         name:Howard Hughes Medical Institute, University of California Berkeley, Berkeley, USA
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         name:Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
         type:PostalAddress
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            address:
               name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
               type:PostalAddress
            type:Organization
            name:Li Ka Shing Centre
            address:
               name:Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
               type:PostalAddress
            type:Organization
      name:Xiao-Yong Li
      affiliation:
            name:Lawrence Berkeley National Laboratory
            address:
               name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
               type:PostalAddress
            type:Organization
            name:University of California Berkeley
            address:
               name:Howard Hughes Medical Institute, University of California Berkeley, Berkeley, USA
               type:PostalAddress
            type:Organization
      name:Jingyi Li
      affiliation:
            name:University of California Berkeley
            address:
               name:Department of Statistics, University of California Berkeley, Berkeley, USA
               type:PostalAddress
            type:Organization
      name:James B Brown
      affiliation:
            name:University of California Berkeley
            address:
               name:Department of Statistics, University of California Berkeley, Berkeley, USA
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            type:Organization
      name:Hou Cheng Chu
      affiliation:
            name:Lawrence Berkeley National Laboratory
            address:
               name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
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            type:Organization
      name:Lucy Zeng
      affiliation:
            name:Lawrence Berkeley National Laboratory
            address:
               name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
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            name:Lawrence Berkeley National Laboratory
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            name:Lawrence Berkeley National Laboratory
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            name:Lawrence Berkeley National Laboratory
            address:
               name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
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            type:Organization
      name:Peter Bickel
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            name:University of California Berkeley
            address:
               name:Department of Statistics, University of California Berkeley, Berkeley, USA
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            type:Organization
      name:Mark D Biggin
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            name:Lawrence Berkeley National Laboratory
            address:
               name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
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            name:University of California Berkeley
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            name:University of California Berkeley
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      email:[email protected]
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      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Howard Hughes Medical Institute, University of California Berkeley, Berkeley, USA
      name:Department of Statistics, University of California Berkeley, Berkeley, USA
      name:Department of Statistics, University of California Berkeley, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Department of Statistics, University of California Berkeley, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
      name:Howard Hughes Medical Institute, University of California Berkeley, Berkeley, USA
      name:Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA

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