The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans
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{"title"=>"The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans", "type"=>"journal", "authors"=>[{"first_name"=>"Eric M.", "last_name"=>"Camino", "scopus_author_id"=>"55904750200"}, {"first_name"=>"John C.", "last_name"=>"Butts", "scopus_author_id"=>"56667159900"}, {"first_name"=>"Alison", "last_name"=>"Ordway", "scopus_author_id"=>"56201587900"}, {"first_name"=>"Jordan E.", "last_name"=>"Vellky", "scopus_author_id"=>"56667638700"}, {"first_name"=>"Mark", "last_name"=>"Rebeiz", "scopus_author_id"=>"6602287695"}, {"first_name"=>"Thomas M.", "last_name"=>"Williams", "scopus_author_id"=>"54997747600"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"604707326", "sgr"=>"84930318800", "issn"=>"15537404", "pmid"=>"25835988", "scopus"=>"2-s2.0-84930318800", "doi"=>"10.1371/journal.pgen.1005136"}, "id"=>"6c654ed3-3384-3531-a7ba-2fbbfc734444", "abstract"=>"The origination and diversification of morphological characteristics represents a key problem in understanding the evolution of development. Morphological traits result from gene regulatory networks (GRNs) that form a web of transcription factors, which regulate multiple cis-regulatory element (CRE) sequences to control the coordinated expression of differentiation genes. The formation and modification of GRNs must ultimately be understood at the level of individual regulatory linkages (i.e., transcription factor binding sites within CREs) that constitute the network. Here, we investigate how elements within a network originated and diversified to generate a broad range of abdominal pigmentation phenotypes among Sophophora fruit flies. Our data indicates that the coordinated expression of two melanin synthesis enzymes, Yellow and Tan, recently evolved through novel CRE activities that respond to the spatial patterning inputs of Hox proteins and the sex-specific input of Bric-à-brac transcription factors. Once established, it seems that these newly evolved activities were repeatedly modified by evolutionary changes in the network's trans-regulators to generate large-scale changes in pigment pattern. By elucidating how yellow and tan are connected to the web of abdominal trans-regulators, we discovered that the yellow and tan abdominal CREs are composed of distinct regulatory inputs that exhibit contrasting responses to the same Hox proteins and Hox cofactors. These results provide an example in which CRE origination underlies a recently evolved novel trait, and highlights how coordinated expression patterns can evolve in parallel through the generation of unique regulatory linkages.", "link"=>"http://www.mendeley.com/research/evolutionary-origination-diversification-dimorphic-gene-regulatory-network-through-parallel-innovati", "reader_count"=>42, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>5, "Researcher"=>8, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>3, "Other"=>3, "Student > Master"=>5, "Student > Bachelor"=>3, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>5, "Researcher"=>8, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>3, "Other"=>3, "Student > Master"=>5, "Student > Bachelor"=>3, "Professor"=>3}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>31, "Neuroscience"=>1, "Chemistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}}, "reader_count_by_country"=>{"Austria"=>1, "Turkey"=>1, "United States"=>1, "France"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2004400"], "description"=>"<p>(A-E) A schematic representation of the male abdomens for several <i>Sophophora</i> species with diverse patterns of pigmentation. (A’-E’) EGFP-reporter transgene expression driven by sequences orthologous to the <i>D</i>. <i>melanogaster</i> t_MSE in transgenic male pupae at ~95 hours after puparium formation. (A’-C’) Sequences from species with male-specific tergite pigmentation drive robust male-specific reporter expression in the A5 and A6 segments, (D’ and E’) whereas the sequences from more distantly related species with monomorphic tergite pigmentation have little-to-no abdominal regulatory activity. (A”-E”) EGFP-reporter transgene expression driven by sequences orthologous to the <i>D</i>. <i>melanogaster yellow</i> wing/body element, here referred to as <i>yellow</i> 5’, in transgenic male pupae at ~85 hours after puparium formation. (A”-C”) Sequences from species with male-specific tergite pigmentation drive robust male-specific reporter expression in the A5 and A6 segments. (D”) The <i>D</i>. <i>pseudoobscura</i> sequence drives pan-abdomen reporter expression. (E”) The <i>D</i>. <i>willistoni</i> sequence lacks abdominal regulatory activity. Blue arrowheads indicate <i>D</i>. <i>auraria</i> reporter expression in transgenic <i>D</i>. <i>melanogaster</i> that extends one segment anterior to the endogenous domain of pigmentation. Red arrowheads indicate the absence of <i>D</i>. <i>malerkotliana</i> reporter expression in the A4 segment of transgenic <i>D</i>. <i>melanogaster</i>, a segment that is endogenously pigmented.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366651, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g002", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tracing_the_ancestry_and_evolution_of_CREs_that_drive_male_specific_tan_and_yellow_expression_/1366651", "title"=>"Tracing the ancestry and evolution of CREs that drive male-specific <i>tan</i> and <i>yellow</i> expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004399"], "description"=>"<p>(A) Phylogenetic relationship between extant <i>Sophophora</i> species. (B-H, B’-H’, and B”-H’) Each image shown is from a male abdomen. Whole-mount images of dorsal fruit fly abdomens from species representing diverse <i>Sophophora</i> lineages. <i>D</i>. <i>melanogaster</i> bears a derived pigmentation pattern on the A5 and A6 tergites, which arose after it diverged from its most recent common ancestor (MRCA) shared with the monomorphically pigmented <i>D</i>. <i>willistoni</i> (node in phylogeny marked “1”) and perhaps after diverging from the MRCA shared with <i>D</i>. <i>pseudoobscura</i> (node “2”). Node 3 represents the MRCA of the <i>melanogaster</i> species group that includes the Oriental lineage (<i>D</i>. <i>melanogaster</i>), <i>montium</i> subgroup (includes <i>D</i>. <i>auraria</i> and <i>D</i>. <i>kikkawai</i>), and <i>ananassae</i> subgroup (includes <i>D</i>. <i>malerkotliana</i> and <i>D</i>. <i>ananassae</i>). This MRCA is suspected to have possessed male-specific tergite pigmentation that is indicated by the hemi-filled in circle. Since its origin, the number of pigmented male tergites has expanded (<i>D</i>. <i>malerkotliana</i>), retracted (<i>D</i>. <i>auraria</i>) and was independently lost (<i>D</i>. <i>kikkawai</i> and <i>D</i>. <i>ananassae</i>; nodes 4 and 5 that are indicated by the circles with a superimposed X). (B’-H’) Abdominal <i>tan</i> mRNA expression shown by <i>in situ</i> hybridization at a developmental stage equivalent to 85–95 hours after puparium formation (APF) for <i>D</i>. <i>melanogaster</i> pupae. (B”-H”) Abdominal <i>yellow</i> mRNA expression shown by <i>in situ</i> hybridization at a developmental stage equivalent to 75–85 hours APF for <i>D</i>. <i>melanogaster</i> pupae. Species are identified by labels at the top of each column.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366650, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g001", "stats"=>{"downloads"=>0, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_between_pigmentation_and_the_gene_expression_of_tan_and_yellow_in_the_Sophophora_subgenus_/1366650", "title"=>"Correlation between pigmentation and the gene expression of <i>tan</i> and <i>yellow</i> in the <i>Sophophora</i> subgenus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004486", "https://ndownloader.figshare.com/files/2004487", "https://ndownloader.figshare.com/files/2004488", "https://ndownloader.figshare.com/files/2004489", "https://ndownloader.figshare.com/files/2004490", "https://ndownloader.figshare.com/files/2004491", "https://ndownloader.figshare.com/files/2004492", "https://ndownloader.figshare.com/files/2004493", "https://ndownloader.figshare.com/files/2004494", "https://ndownloader.figshare.com/files/2004495", "https://ndownloader.figshare.com/files/2004496", "https://ndownloader.figshare.com/files/2004497", "https://ndownloader.figshare.com/files/2004498", "https://ndownloader.figshare.com/files/2004499", "https://ndownloader.figshare.com/files/2004500", "https://ndownloader.figshare.com/files/2004501"], "description"=>"<div><p>The origination and diversification of morphological characteristics represents a key problem in understanding the evolution of development. Morphological traits result from gene regulatory networks (GRNs) that form a web of transcription factors, which regulate multiple <i>cis</i>-regulatory element (CRE) sequences to control the coordinated expression of differentiation genes. The formation and modification of GRNs must ultimately be understood at the level of individual regulatory linkages (i.e., transcription factor binding sites within CREs) that constitute the network. Here, we investigate how elements within a network originated and diversified to generate a broad range of abdominal pigmentation phenotypes among <i>Sophophora</i> fruit flies. Our data indicates that the coordinated expression of two melanin synthesis enzymes, Yellow and Tan, recently evolved through novel CRE activities that respond to the spatial patterning inputs of Hox proteins and the sex-specific input of Bric-à-brac transcription factors. Once established, it seems that these newly evolved activities were repeatedly modified by evolutionary changes in the network’s <i>trans</i>-regulators to generate large-scale changes in pigment pattern. By elucidating how <i>yellow</i> and <i>tan</i> are connected to the web of abdominal <i>trans</i>-regulators, we discovered that the <i>yellow</i> and <i>tan</i> abdominal CREs are composed of distinct regulatory inputs that exhibit contrasting responses to the same Hox proteins and Hox cofactors. These results provide an example in which CRE origination underlies a recently evolved novel trait, and highlights how coordinated expression patterns can evolve in parallel through the generation of unique regulatory linkages.</p></div>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366696, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005136.s001", "https://dx.doi.org/10.1371/journal.pgen.1005136.s002", "https://dx.doi.org/10.1371/journal.pgen.1005136.s003", "https://dx.doi.org/10.1371/journal.pgen.1005136.s004", "https://dx.doi.org/10.1371/journal.pgen.1005136.s005", "https://dx.doi.org/10.1371/journal.pgen.1005136.s006", "https://dx.doi.org/10.1371/journal.pgen.1005136.s007", "https://dx.doi.org/10.1371/journal.pgen.1005136.s008", "https://dx.doi.org/10.1371/journal.pgen.1005136.s009", "https://dx.doi.org/10.1371/journal.pgen.1005136.s010", "https://dx.doi.org/10.1371/journal.pgen.1005136.s011", "https://dx.doi.org/10.1371/journal.pgen.1005136.s012", "https://dx.doi.org/10.1371/journal.pgen.1005136.s013", "https://dx.doi.org/10.1371/journal.pgen.1005136.s014", "https://dx.doi.org/10.1371/journal.pgen.1005136.s015", "https://dx.doi.org/10.1371/journal.pgen.1005136.s016"], "stats"=>{"downloads"=>30, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Evolutionary_Origination_and_Diversification_of_a_Dimorphic_Gene_Regulatory_Network_through_Parallel_Innovations_in_cis_and_trans_/1366696", "title"=>"The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in <i>cis</i> and <i>trans</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004414"], "description"=>"<p>Wiring diagram of pigmentation gene networks experienced by the (A) non-melanic male A2-A4 segments and (B) the melanic A5 and A6 segments. (A) Abd-B expression is lacking in the anterior A2-A4 segments and as a result <i>yellow</i> and <i>tan</i> lack the direct and indirect activating input from this transcription factor. In these segments, Abd-A forms direct repressive inputs with <i>tan</i> which are supported (directly or indirectly) by the repressive effects of <i>exd</i> and <i>hth</i>. (B) Abd-B is expressed in the posterior A5 and A6 segments, where it acts as a direct activator of <i>yellow</i> and an indirect activator of <i>tan</i>. In these segments, Abd-A acts as an indirect activator of <i>tan</i> expression as well. In these schematics, inactive genes are indicated in gray coloring, solid connections between genes indicate validated direct interactions between a transcription factor and a pigmentation gene CRE, and dashed connections indicate indirect interactions or those not yet shown to be direct. Connections terminating with an arrowhead indicate connections in which the transcription factor functions as an activator, and connections terminating in a nail head shape indicate a repressive relationship.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366659, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g007", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_network_models_for_unpigmented_and_pigment_abdominal_segments_/1366659", "title"=>"Gene network models for unpigmented and pigment abdominal segments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004402"], "description"=>"<p>(A-F) EGFP reporter expression driven by the t_MSE was imaged at ~95 hours after puparium formation in male pupae. (A’-F’) EGFP reporter expression driven by the yBE0.6 was imaged at ~85 hours after puparium formation in male pupae. (A”-F”) EGFP reporter expression driven by the <i>yellow</i> 5’ sequence was imaged at ~85 hours after puparium formation in male pupae. Genotypes altering the genetic background are listed at the top of each column. Specimens are (A, A’, and A”‘) homozygous and (B-F, B’-F’, and B”-F”) hemizygous for the EGFP reporter transgene. (B) t_MSE, (B’) yBE0.6, and (B”) <i>yellow</i> 5’ regulatory activity expands into the A3 and A4 segments where <i>Abd-B</i> is ectopically expressed. Compared to a (C) control genetic background, the (D) t_MSE regulatory activity is dramatically reduced in the midline region where <i>abd-A</i> expression is suppressed. Suppression of (E) <i>hth</i> and (F) <i>exd</i> expression results in ectopic t_MSE regulatory activity in the A4 and A3 segments. Suppression of (D’) <i>abd-A</i>, (E’) <i>hth</i>, and (F’) <i>exd</i> expression has little-to-no effect on yBE0.6 regulatory activity compared to the (C’) control genetic background. Suppression of (D”) <i>abd-A</i> and (F”) <i>exd</i> has little-to-effect on the <i>yellow</i> 5’ regulatory activity compared to the (C”) control genetic background. Suppression of (E”) <i>hth</i> results in a mild expansion of regulatory activity into the A3 and A4 segments. Blue arrowheads indicate segments where the genetic background modification resulted in ectopic reporter transgene activity. Red arrowheads indicate segments where the genetic background modification resulted in a loss of reporter transgene activity.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366653, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g004", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_interactions_between_pigmentation_network_transcription_factors_and_CREs_regulating_abdominal_tan_and_yellow_expression_/1366653", "title"=>"Genetic interactions between pigmentation network transcription factors and CREs regulating abdominal <i>tan</i> and <i>yellow</i> expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004401"], "description"=>"<p>(A and B) A schematic representation of the male abdomens for two species with derived losses in male pigmentation. (A’ and B’) EGFP-reporter transgene expression driven by sequences orthologous to the <i>D</i>. <i>melanogaster</i> t_MSE in transgenic male pupae at ~95 hours after puparium formation. (A’) The <i>D</i>. <i>kikkawai</i> sequence possesses robust male-specific regulatory activity in the A5 and A6 segments, (B’) whereas the <i>D</i>. <i>ananassae</i> sequence has little-to-no abdominal regulatory activity. (A” and B”) EGFP-reporter transgene expression driven by sequences orthologous to the <i>D</i>. <i>melanogaster yellow</i> wing/body element in transgenic male pupae at ~85 hours after puparium formation. (A”) The <i>D</i>. <i>kikkawai</i> sequence retains the posterior stripe regulatory activities characteristic of the wing element but lacks the body element’s male-specific activity. (B”) The <i>D</i>. <i>ananassae</i> sequence possesses the regulatory activities characteristic of the wing element and body element. Red arrowheads indicate segments in which the regulatory activity is lacking.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366652, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g003", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tracing_the_CRE_bases_for_losses_in_male_tergite_pigmentation_/1366652", "title"=>"Tracing the CRE bases for losses in male tergite pigmentation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004415"], "description"=>"<p>A pigmentation enzyme gene perspective of network evolution.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366660, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.t001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_pigmentation_enzyme_gene_perspective_of_network_evolution_/1366660", "title"=>"A pigmentation enzyme gene perspective of network evolution.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004412"], "description"=>"<p>(A) The SM6 region of the t_MSE possesses five sites, S1-S5, with sequences characteristic of Abd-B (TTAT) and Abd-A (TAAT) binding sites. This CRE region also possesses sites resembling sequences bound by Exd and Hth, though the functionality of the Exd site was not studied here. (B-F) EGFP reporter transgene expression in male pupae at ~95 hours after puparium formation. (B) The t_MSE2 sequence drives robust expression in the male A5 and A6 segments. When all of the (C) TTAT sites and (D) TTAT and TAAT sites depicted in (A) were mutated, regulatory activity in the male A5 segment was reduced to 89±6% and 88±3% respectively. (F) When the entire SM6 region was mutated, regulatory activity decreased to 31±1%. (C) The TTAT site mutations resulted in activity increasing in the A4 and A3 segments respectively to 169±4% and 261±6%. (D) The TTAT and TAAT site mutations resulted in activity increasing in the A4 and A3 segments respectively to 207±2% and 281±2%. (E) When the Hth site was mutated, regulatory activity in the male A5, A4, and A3 segments respectively increased to 122±7%, 236±6%, and 276±4%.(F) The entire SM6 region mutation resulted in activity decreasing in the A4 and A3 segments respectively to 64±1% and 73±1%. Blue arrowheads indicate segments where activity was notably increased and Red arrowheads indicate segments with notably decreased activity compared to the wild type sequence. Gel shift assays for sequences possessing wild type and mutant site (G) 3, (H) 4, and (I) 5 and the DNA-binding domains for Abd-A and Abd-B. Binding reactions used increasing amounts of the GST-DNA binding domain fusion protein (from left to right: 0 ng, 111 ng, 333 ng, 1000 ng, and 3000 ng). Binding correlated with the amount of input protein for the probes with the non-mutant sequence, whereas binding was dramatically reduced for the probes with a mutant Hox site.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366657, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g006", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_the_direct_Hox_inputs_shaping_tan_expression_/1366657", "title"=>"Characterization of the direct Hox inputs shaping <i>tan</i> expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2004410"], "description"=>"<p>(A) Ten scanning mutant versions, SM1-SM10, of the <i>D</i>. <i>melanogaster</i> yBE0.6 sequence and t_MSE sequence were created. In each mutant, a block of ~70 base pairs was altered such that every other nucleotide was altered by a non-complementary nucleotide transversion. (B-G) EGFP reporter transgene expression in <i>D</i>. <i>melanogaster</i> male pupae at ~85 hours after puparium formation. (B) The yBE0.6 sequence drives reporter expression in the male A5 and A6 segments. (C and D) The SM2 and SM3 mutations resulted in a modest reduction in regulatory activity, whereas the (F and G) SM5 and SM6 mutations resulted in a near-total loss of reporter activity. (E) The SM4 mutation led to a pan-abdomen increase in regulatory activity. (H-J) EGFP reporter transgene expression in <i>D</i>. <i>melanogaster</i> male pupae at ~95 hours after puparium formation. (H) The t_MSE sequence drives expression in the male A5 and A6 segments. (I and J) The SM5 and SM6 mutations resulted in a loss of reporter expression in the male abdomen. Red arrowheads indicate regions where the regulatory activity was greatly reduced due to a scanning mutation and the Orange arrowheads indicate regions where regulatory activity was modestly reduced. Blue arrowheads indicate regions where regulatory activity was gained due to a scanning mutation.</p>", "links"=>[], "tags"=>["web", "novel CRE activities", "factor", "origination", "Hox proteins", "melanin synthesis enzymes", "pattern", "grn", "Morphological traits result", "gene", "expression", "Dimorphic Gene Regulatory Network", "linkage", "transcription"], "article_id"=>1366655, "categories"=>["Biological Sciences"], "users"=>["Eric M. Camino", "John C. Butts", "Alison Ordway", "Jordan E. Vellky", "Mark Rebeiz", "Thomas M. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005136.g005", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scanning_mutagenesis_identifies_CRE_sequences_required_for_yellow_and_tan_expression_/1366655", "title"=>"Scanning mutagenesis identifies CRE sequences required for <i>yellow</i> and <i>tan</i> expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 16:08:58"}

PMC Usage Stats | Further Information

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Relative Metric

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