In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA
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{"title"=>"In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA", "type"=>"journal", "authors"=>[{"first_name"=>"Janet L.", "last_name"=>"Smith", "scopus_author_id"=>"56826465200"}, {"first_name"=>"Alan D.", "last_name"=>"Grossman", "scopus_author_id"=>"7202301077"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537404", "pui"=>"604817928", "pmid"=>"26020636", "isbn"=>"1553-7390\r1553-7404", "doi"=>"10.1371/journal.pgen.1005258", "sgr"=>"84930797954", "scopus"=>"2-s2.0-84930797954"}, "id"=>"e117558a-ffd0-3f34-92fb-329b71db785f", "abstract"=>"DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA in vivo, suggesting that other cellular factors or the amount of available DnaA in vivo restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA in vivo but not in vitro, and that the nucleoid-associated protein Rok was required for binding in vivo. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.", "link"=>"http://www.mendeley.com/research/vitro-whole-genome-dna-binding-analysis-bacterial-replication-initiator-transcription-factor-dnaa", "reader_count"=>42, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>27, "Chemistry"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Denmark"=>1, "United Kingdom"=>1, "France"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2086985"], "description"=>"<p>Histograms of the number of sequence reads that start at each nucleotide are plotted as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.g002\" target=\"_blank\">Fig 2</a> (blue, above the line, for sequence reads mapping to the top strand; green, below the line, for sequence reads mapping to the bottom strand). Data are from a binding reaction containing 4.1 μM ATP-DnaA-his, except for panel <i>F</i>, where data are from a reaction containing 55 nM ATP-DnaA-his. For each panel, a 300 bp portion of the genome is presented, and the y-axis is scaled so that the data fills the space. Predicted DnaA boxes are represented by red ovals, and are numbered from left to right for regions with more than three DnaA boxes. The gray rectangles below the histograms depict nearby genes, with arrowheads indicating the direction of transcription. The regions presented are: <i>(A)</i> inside <i>cssS</i>; <i>(B)</i> inside <i>ygaN</i>; <i>(C)</i> inside <i>ypiF</i>; <i>(D)</i> inside <i>lpdV</i>; <i>(E)</i> inside <i>yabS</i>; <i>(F)</i> upstream of <i>sda</i> (55 nM ATP-DnaA-his data); <i>(G)</i> upstream of <i>sda</i> (4.1 μM ATP-DnaA-his data). Panel B corresponds to peak #140 (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s007\" target=\"_blank\">S1 Table</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s007\" target=\"_blank\">S1 Fig</a>) and panels F and G correspond to peak #7. The other regions did not show sufficient binding at 1.4 μM DnaA to be included in the peak catalog.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429664, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_DnaA_binding_sites_at_single_nucleotide_resolution_/1429664", "title"=>"Identification of DnaA binding sites at single nucleotide resolution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086987"], "description"=>"<p><i>(A)</i> A logo, drawn using WebLogo [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.ref032\" target=\"_blank\">32</a>], of the DnaA boxes used to construct the DnaA box PSSM is shown. <i>(B-E)</i> Histograms of the number of sequence reads that start at each nucleotide are plotted (blue for sequence reads mapping to the top strand; green for sequence reads mapping to the bottom strand). Data are from the binding reaction containing 4.1 μM ATP-DnaA-his. For each panel, a 300 bp portion of the genome is presented, and the y-axes are scaled so that the data fills the space. The red ovals on the horizontal axis indicate the position of DnaA binding sites predicted using the PSSM described here. The pink ovals above the horizontal axis indicate DnaA boxes with 2 mismatches from the TTATNCACA consensus sequence, and the maroon ovals have 1 mismatch from the TTATNCACA consensus. (No perfect matches to the consensus are found in these regions.) The gray rectangles below the histograms indicate nearby genes, with arrowheads indicating the direction of transcription.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429666, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.g004", "stats"=>{"downloads"=>2, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_DnaA_boxes_from_a_consensus_sequence_with_DnaA_boxes_from_the_PSSM_/1429666", "title"=>"Comparison of DnaA boxes from a consensus sequence with DnaA boxes from the PSSM.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086989"], "description"=>"<p>The relative amount of DNA recovered from different chromosomal regions is plotted on the y-axis, versus the ATP-DnaA-his concentration on the x-axis. The curves were obtained from fitting the data to the Hill Equation. Chromosomal locations (nucleotide position in the sequence of AG1839, peak number in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s002\" target=\"_blank\">S1 Table</a>, and nearby genes) include: <i>(A)</i> 150, #1, upstream of <i>rpmH</i> and <i>dnaA</i>; <i>(B)</i> 1841, #2, downstream of <i>dnaA</i> and upstream of the DUE and <i>dnaN</i>; <i>(C)</i> 3885674, #5, upstream of <i>ywcI</i> and <i>vpr</i>; <i>(D)</i> 627955, #3, downstream of <i>gcp</i> and <i>ydiF</i>; <i>(E)</i> 4191071, #4, upstream of <i>trmE</i> and downstream of <i>jag</i>; <i>(F)</i> 3772105, #6, upstream of <i>ywlC</i> and downstream of <i>ywlB</i>; <i>(G)</i> 2620059, #7, upstream of <i>yqeG</i> and <i>sda</i>; <i>(H)</i> 4113012, #8, upstream of <i>yydA</i> and downstream of <i>yyzF</i>; <i>(I)</i> 1670814, #9, inside <i>codV</i>; <i>(J)</i> 137727, #10, inside <i>rplB</i>; <i>(K)</i> 624773, #40, inside <i>thiL</i>; <i>(L)</i> 1922157, #127, upstream of <i>ynfC</i> and <i>alsT</i>.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429668, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.g005", "stats"=>{"downloads"=>14, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_curves_for_ATP_DnaA_his_for_selected_chromosomal_regions_/1429668", "title"=>"Binding curves for ATP-DnaA-his for selected chromosomal regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086990"], "description"=>"<p><i>(A)</i> The ratio of the amount of DNA recovered bound to ATP-DnaA-his vs. ADP-DnaA-his is plotted versus the DnaA concentration. Background binding was subtracted prior to calculating the ratio. All 269 peaks detected at 1.4 μM were analyzed at each concentration, but the ratio of ATP/ADP binding is shown only if the binding was 1.5-times greater than background for both the ATP and the ADP binding reactions at that DnaA-his concentration. For many weaker peaks, these criteria were met only at the highest concentration of DnaA-his. Solid and dotted lines connect points for the indicated region across concentrations. The black bars indicate the average ratio (ATP-DnaA-his/ADP-DnaA-his) at each DnaA-his concentration. The two data points at 1.4 μM DnaA-his that are slightly less than 1 correspond to the <i>yydA</i> and <i>dnaN</i> regions. <i>(B-G)</i> The relative amount of DNA recovered from different chromosomal regions is plotted on the y-axis, versus the DnaA-his concentration (log scale) on the x-axis. ATP-DnaA-his, open circles and dashed lines (data are the same as shown in parts of <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.g005\" target=\"_blank\">Fig 5</a>); ADP-DnaA-his, filled triangles and dotted lines. Genomic coordinates (AG1839 genome), and nearby genes: <i>(B)</i> 2620051, upstream of <i>sda</i> and <i>yqeG</i>; <i>(C)</i> 627955, downstream of <i>gcp</i> and <i>ydiF</i>; <i>(D)</i> 972751, inside <i>yhcN</i>; <i>(E)</i> 1006129, inside <i>yhdF</i>; <i>(F)</i> 150, <i>oriC</i> upstream of <i>dnaA</i>; <i>(G)</i> 1841, <i>oriC</i> upstream of the DUE and <i>dnaN</i>.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429669, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.g006", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_DNA_binding_by_ATP_DnaA_his_compared_to_ADP_DnaA_his_/1429669", "title"=>"Relative DNA binding by ATP-DnaA-his compared to ADP-DnaA-his.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086991"], "description"=>"<p><sup>1</sup>The two binding regions in <i>oriC</i> are listed first, and subsequent peaks are ordered by the amounts of DNA recovered at 1.4 μM ATP-DnaA-his. For peaks in intergenic regions, both flanking genes are indicated. For peaks located within genes, only that gene is indicated.</p><p><sup>2</sup>The numbers presented are the genome coordinates for the summit of each peak. The genome sequence used was from lab strain AG1839 [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.ref029\" target=\"_blank\">29</a>] with 1 being the nucleotide 409 bp upstream of the <i>dnaA</i> open reading frame.</p><p><sup>3</sup>The number of putative DnaA binding sites (DnaA boxes) in a 300 bp window centered on the peak summit, as determined using the PSSM (Materials and Methods).</p><p><sup>4</sup>Apparent K<sub>d</sub>’s were determined as described (Materials and Methods) and are indicated for ATP-DnaA-his (ATP) and ADP-DnaA-his (ADP).</p><p>Top 20 DnaA binding regions <i>in vitro</i>.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429670, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.t001", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_20_DnaA_binding_regions_in_vitro_/1429670", "title"=>"Top 20 DnaA binding regions <i>in vitro</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086992"], "description"=>"<p><sup>1</sup> Wild type (<i>rok</i>+; AG174) and a <i>rok</i> null mutant (<i>rok</i>-; HM57) were grown to mid-exponential phase in LB medium. Crosslinking, immunoprecipitation with anti-DnaA antibodies, and PCR with primers to the indicated chromosomal regions were done as described (Materials and Methods). Numbers indicate the fold enrichment of the indicated chromosomal regions in the immunoprecipitate compared to a control chromosomal region ± standard deviation from six independent cultures. P values are from a one-sided Student’s t-Test. The effects of <i>rok</i> on DnaA binding are significant at all loci indicated, except for <i>dnaA</i>.</p><p>Effects of Rok on binding by DnaA in vivo<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#t002fn001\" target=\"_blank\"><sup>1</sup></a>.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429671, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.t002", "stats"=>{"downloads"=>8, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effects_of_Rok_on_binding_by_DnaA_in_vivo_1_/1429671", "title"=>"Effects of Rok on binding by DnaA in vivo<sup>1</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2087000", "https://ndownloader.figshare.com/files/2087001", "https://ndownloader.figshare.com/files/2087002", "https://ndownloader.figshare.com/files/2087003", "https://ndownloader.figshare.com/files/2087004", "https://ndownloader.figshare.com/files/2087005", "https://ndownloader.figshare.com/files/2087006", "https://ndownloader.figshare.com/files/2087007", "https://ndownloader.figshare.com/files/2087008", "https://ndownloader.figshare.com/files/2087009", "https://ndownloader.figshare.com/files/2087010", "https://ndownloader.figshare.com/files/2087011"], "description"=>"<div><p>DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of <i>Bacillus subtilis</i> DnaA to genomic DNA <i>in vitro</i> at single nucleotide resolution using <i>in vitro</i> DNA affinity purification and deep sequencing (IDAP-Seq). We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA <i>in vivo</i>, suggesting that other cellular factors or the amount of available DnaA <i>in vivo</i> restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA <i>in vivo</i> but not <i>in vitro</i>, and that the nucleoid-associated protein Rok was required for binding <i>in vivo</i>. Our <i>in vitro</i> characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on <i>in vivo</i> binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.</p></div>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429679, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005258.s001", "https://dx.doi.org/10.1371/journal.pgen.1005258.s002", "https://dx.doi.org/10.1371/journal.pgen.1005258.s003", "https://dx.doi.org/10.1371/journal.pgen.1005258.s004", "https://dx.doi.org/10.1371/journal.pgen.1005258.s005", "https://dx.doi.org/10.1371/journal.pgen.1005258.s006", "https://dx.doi.org/10.1371/journal.pgen.1005258.s007", "https://dx.doi.org/10.1371/journal.pgen.1005258.s008", "https://dx.doi.org/10.1371/journal.pgen.1005258.s009", "https://dx.doi.org/10.1371/journal.pgen.1005258.s010", "https://dx.doi.org/10.1371/journal.pgen.1005258.s011", "https://dx.doi.org/10.1371/journal.pgen.1005258.s012"], "stats"=>{"downloads"=>28, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_Vitro_Whole_Genome_DNA_Binding_Analysis_of_the_Bacterial_Replication_Initiator_and_Transcription_Factor_DnaA/1429679", "title"=>"<i>In Vitro</i> Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086982"], "description"=>"<p>The relative amount of binding by ATP-DnaA-his is plotted on the y-axis (normalized so that maximum binding has an amplitude of 1) versus the position along the chromosome on the x-axis. The amount of binding was determined by sequence analysis of the DNA recovered in each binding reaction. Binding data is presented in 200 nucleotide bins, with the maximum binding amplitude in each bin drawn. The 4.2 mb circular chromosome is depicted linearly such that the origin of replication is near the middle of the x-axis. The concentration of ATP-DnaA-his in each binding reaction was <i>(A)</i> no DnaA; <i>(B)</i> 55 nM; <i>(C)</i> 140 nM; <i>(D)</i> 550 nM; <i>(E)</i> 1.4 μM; <i>(F)</i> 4.1 μM. The major peaks are numbered <i>(C)</i>, and correspond to the following nearby loci: (1) <i>sda</i>; (2) <i>ywlC</i>; (3) <i>ywc</i>I; (4) <i>yydA</i>; (5) consists of 3 adjacent peaks (<i>trmE</i>, <i>dnaA</i>, and between <i>dnaA</i> and <i>dnaN</i>) that are not resolved at this scale; (6) <i>gcp</i>/<i>ydiF</i>. The inset in panel B above the asterisk corresponds to a 7 kb region that contains the <i>trmE</i>, <i>dnaA</i>, and <i>dnaA/N</i> binding regions.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429661, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.g001", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_of_ATP_DnaA_his_to_genomic_DNA_in_vitro_/1429661", "title"=>"Binding of ATP-DnaA-his to genomic DNA <i>in vitro</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 04:17:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/2086984"], "description"=>"<p>The 10 strongest binding regions <i>(A-J)</i>, plus one weaker binding region <i>(K</i>, <i>L)</i>, are displayed, using binding data at 1.4 μM ATP-DnaA-his. The bottom section of each panel shows the genomic coordinates (using the AG1839 genomic sequence), the positions of each gene (gray rectangles), and the gene names. Arrowheads indicate the direction of transcription. The middle section of each panel is a histogram of the number of sequence reads that start at each nucleotide (blue, above the line, for sequence reads mapping to the top strand; green, below the line, for sequence reads mapping to the bottom strand). The red circles indicate DnaA boxes, predicted using the PSSM described in this paper. The top section of each panel is a plot of the amount of DNA recovered (as inferred from the sequence data) versus genome position, using 1.4 μM ATP-DnaA-his (black line) or no DnaA (red lines). The amount of DNA recovered is scaled to a global maximum of 1, as described for <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.g001\" target=\"_blank\">Fig 1</a>. <i>A-J</i>. The 10 strongest binding regions, corresponding to peaks #1–10 in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.t001\" target=\"_blank\">Table 1</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s002\" target=\"_blank\">S1 Table</a>, and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s007\" target=\"_blank\">S1 Fig</a>. <i>(A)</i> upstream of <i>dnaA</i> (part of <i>oriC</i>); <i>(B)</i> between <i>dnaA</i> and <i>dnaN</i>, containing the DNA unwinding element (also part of <i>oriC</i>); <i>(C)</i> upstream of <i>ywcI</i> and <i>vpr</i>; <i>(D)</i> downstream of <i>gcp</i> and <i>ydiF</i>; <i>(E)</i> upstream of <i>trmE</i> and downstream of <i>jag</i>; <i>(F)</i> upstream of <i>ywlC</i> and downstream of <i>ywlB</i>; <i>(G)</i> upstream of <i>yqeG</i> and <i>sda</i>; <i>(H)</i> upstream of <i>yydA</i>, spanning <i>yyzF</i>, and upstream of <i>yycS</i>; <i>(I)</i> within <i>codV</i>; <i>(J)</i> within <i>rplB</i>. <i>K-L</i>. A representative weaker binding region, (peak #49 in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s002\" target=\"_blank\">S1 Table</a>; <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005258#pgen.1005258.s007\" target=\"_blank\">S1 Fig</a>). <i>(K)</i> binding scaled to 1 to be comparable to previous panels; <i>(L)</i> the same region rescaled so that the binding pattern is visible.</p>", "links"=>[], "tags"=>["aaa", "Transcription Factor DnaA DnaA", "atp", "DNA binding proteins", "vivo", "Genome DNA Binding Analysis", "DNA affinity purification", "DnaA binding site", "Bacillus subtilis DnaA", "chromosomal regions", "replication initiation protein", "nucleotide resolution", "269 binding regions", "Bacterial Replication Initiator"], "article_id"=>1429663, "categories"=>["Biological Sciences"], "users"=>["Janet L. Smith", "Alan D. Grossman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005258.g002", "stats"=>{"downloads"=>3, "page_views"=>52, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IDAP_Seq_data_for_individual_regions_bound_by_DnaA_/1429663", "title"=>"IDAP-Seq data for individual regions bound by DnaA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-28 04:17:46"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"13", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"7", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"2", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"33", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"15", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"6", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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