An Insulator Element Located at the Cyclin B1 Interacting Protein 1 Gene Locus Is Highly Conserved among Mammalian Species
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{"title"=>"An insulator element located at the cyclin B1 interacting protein 1 gene locus is highly conserved among mammalian species", "type"=>"journal", "authors"=>[{"first_name"=>"Wataru", "last_name"=>"Yoshida", "scopus_author_id"=>"13606976600"}, {"first_name"=>"Junko", "last_name"=>"Tomikawa", "scopus_author_id"=>"34769444200"}, {"first_name"=>"Makoto", "last_name"=>"Inaki", "scopus_author_id"=>"23018406300"}, {"first_name"=>"Hiroshi", "last_name"=>"Kimura", "scopus_author_id"=>"56735099000"}, {"first_name"=>"Masafumi", "last_name"=>"Onodera", "scopus_author_id"=>"7004307439"}, {"first_name"=>"Kenichiro", "last_name"=>"Hata", "scopus_author_id"=>"55726787600"}, {"first_name"=>"Kazuhiko", "last_name"=>"Nakabayashi", "scopus_author_id"=>"7101927819"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"26110280", "doi"=>"10.1371/journal.pone.0131204", "sgr"=>"84938319404", "scopus"=>"2-s2.0-84938319404", "issn"=>"19326203", "pui"=>"605398338"}, "id"=>"6a8ffb5e-6345-3dbd-a5ee-fca3a37ebbba", "abstract"=>"Insulators are cis-elements that control the direction of enhancer and silencer activities (enhancer-blocking) and protect genes from silencing by heterochromatinization (barrier activity). Understanding insulators is critical to elucidate gene regulatory mechanisms at chromosomal domain levels. Here, we focused on a genomic region upstream of the mouse Ccnb1ip1 (cyclin B1 interacting protein 1) gene that was methylated in E9.5 embryos of the C57BL/6 strain, but unmethylated in those of the 129X1/SvJ and JF1/Ms strains. We hypothesized the existence of an insulator-type element that prevents the spread of DNA methylation within the 1.8 kbp segment, and actually identified a 242-bp and a 185-bp fragments that were located adjacent to each other and showed insulator and enhancer activities, respectively, in reporter assays. We designated these genomic regions as the Ccnb1ip1 insulator and the Ccnb1ip1 enhancer. The Ccnb1ip1 insulator showed enhancer-blocking activity in the luciferase assays and barrier activity in the colony formation assays. Further examination of the Ccnb1ip1 locus in other mammalian species revealed that the insulator and enhancer are highly conserved among a wide variety of species, and are located immediately upstream of the transcriptional start site of Ccnb1ip1. These newly identified cis-elements may be involved in transcriptional regulation of Ccnb1ip1, which is important in meiotic crossing-over and G2/M transition of the mitotic cell cycle.", "link"=>"http://www.mendeley.com/research/insulator-element-located-cyclin-b1-interacting-protein-1-gene-locus-highly-conserved-among-mammalia", "reader_count"=>4, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2148684", "https://ndownloader.figshare.com/files/2148685", "https://ndownloader.figshare.com/files/2148686", "https://ndownloader.figshare.com/files/2148687", "https://ndownloader.figshare.com/files/2148688", "https://ndownloader.figshare.com/files/2148689", "https://ndownloader.figshare.com/files/2148690", "https://ndownloader.figshare.com/files/2148691", "https://ndownloader.figshare.com/files/2148692", "https://ndownloader.figshare.com/files/2148693", "https://ndownloader.figshare.com/files/2148694", "https://ndownloader.figshare.com/files/2148695", "https://ndownloader.figshare.com/files/2148696"], "description"=>"<div><p>Insulators are <i>cis</i>-elements that control the direction of enhancer and silencer activities (enhancer-blocking) and protect genes from silencing by heterochromatinization (barrier activity). Understanding insulators is critical to elucidate gene regulatory mechanisms at chromosomal domain levels. Here, we focused on a genomic region upstream of the mouse <i>Ccnb1ip1</i> (cyclin B1 interacting protein 1) gene that was methylated in E9.5 embryos of the C57BL/6 strain, but unmethylated in those of the 129X1/SvJ and JF1/Ms strains. We hypothesized the existence of an insulator-type element that prevents the spread of DNA methylation within the 1.8 kbp segment, and actually identified a 242-bp and a 185-bp fragments that were located adjacent to each other and showed insulator and enhancer activities, respectively, in reporter assays. We designated these genomic regions as the <i>Ccnb1ip1</i> insulator and the <i>Ccnb1ip1</i> enhancer. The <i>Ccnb1ip1</i> insulator showed enhancer-blocking activity in the luciferase assays and barrier activity in the colony formation assays. Further examination of the <i>Ccnb1ip1</i> locus in other mammalian species revealed that the insulator and enhancer are highly conserved among a wide variety of species, and are located immediately upstream of the transcriptional start site of <i>Ccnb1ip1</i>. These newly identified cis-elements may be involved in transcriptional regulation of <i>Ccnb1ip1</i>, which is important in meiotic crossing-over and G2/M transition of the mitotic cell cycle.</p></div>", "links"=>[], "tags"=>["mitotic cell cycle", "cyclin B 1", "JF", "Ccnb 1ip", "1.8 kbp segment", "Cyclin B 1 Interacting Protein 1 Gene Locus", "chromosomal domain levels", "barrier activity", "gene", "dna", "Ccnb 1ip enhancer", "C 57BL strain", "Mammalian Species Insulators", "Ccnb 1ip locus", "mouse Ccnb 1ip", "colony formation assays", "Ccnb 1ip insulator", "E 9.5 embryos"], "article_id"=>1463561, "categories"=>["Uncategorised"], "users"=>["Wataru Yoshida", "Junko Tomikawa", "Makoto Inaki", "Hiroshi Kimura", "Masafumi Onodera", "Kenichiro Hata", "Kazuhiko Nakabayashi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0131204.s001", "https://dx.doi.org/10.1371/journal.pone.0131204.s002", "https://dx.doi.org/10.1371/journal.pone.0131204.s003", "https://dx.doi.org/10.1371/journal.pone.0131204.s004", "https://dx.doi.org/10.1371/journal.pone.0131204.s005", "https://dx.doi.org/10.1371/journal.pone.0131204.s006", "https://dx.doi.org/10.1371/journal.pone.0131204.s007", "https://dx.doi.org/10.1371/journal.pone.0131204.s008", "https://dx.doi.org/10.1371/journal.pone.0131204.s009", "https://dx.doi.org/10.1371/journal.pone.0131204.s010", "https://dx.doi.org/10.1371/journal.pone.0131204.s011", "https://dx.doi.org/10.1371/journal.pone.0131204.s012", "https://dx.doi.org/10.1371/journal.pone.0131204.s013"], "stats"=>{"downloads"=>19, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_Insulator_Element_Located_at_the_Cyclin_B1_Interacting_Protein_1_Gene_Locus_Is_Highly_Conserved_among_Mammalian_Species_/1463561", "title"=>"An Insulator Element Located at the Cyclin B1 Interacting Protein 1 Gene Locus Is Highly Conserved among Mammalian Species", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-25 02:46:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/2148682"], "description"=>"<p>RT-PCR products from exon 1 to exon 5 were detected in an E9.5 embryo of JF1. Exon 1 of <i>Ccnb1ip1</i> was located in the vicinity of the <i>Ccnb1ip1</i> insulator (red box) and enhancer (blue box) in the JF1 genome. The sequences corresponding to exon 2 and exon 4 of the <i>Ccnb1ip1</i> gene were found to be present, but those corresponding to exon 1 and exon 3 to be absent (deleted) in the B6 genome. The horizon bars (1 to 7) indicate genomic regions for which DNA methylation statuses were assessed (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131204#pone.0131204.g001\" target=\"_blank\">Fig 1</a>).</p>", "links"=>[], "tags"=>["mitotic cell cycle", "cyclin B 1", "JF", "Ccnb 1ip", "1.8 kbp segment", "Cyclin B 1 Interacting Protein 1 Gene Locus", "chromosomal domain levels", "barrier activity", "gene", "dna", "Ccnb 1ip enhancer", "C 57BL strain", "Mammalian Species Insulators", "Ccnb 1ip locus", "mouse Ccnb 1ip", "colony formation assays", "Ccnb 1ip insulator", "E 9.5 embryos"], "article_id"=>1463559, "categories"=>["Uncategorised"], "users"=>["Wataru Yoshida", "Junko Tomikawa", "Makoto Inaki", "Hiroshi Kimura", "Masafumi Onodera", "Kenichiro Hata", "Kazuhiko Nakabayashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0131204.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Exon_intron_structure_of_the_Ccnb1ip1_gene_in_the_JF1_and_C57BL_6_genomes_/1463559", "title"=>"Exon-intron structure of the <i>Ccnb1ip1</i> gene in the JF1 and C57BL/6 genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 02:46:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/2148683"], "description"=>"<p>The 1,878 bp fragment that contains the human sequences homologous to the mouse <i>Ccnb1ip1</i> insulator and enhancer was cloned in the pGL4.23 [luc2/minP] vector (a) in the sense (b) and the antisense (c) orientations. Two partial fragments, a 975 bp fragment containing both putative insulator and enhancer, and a 1,207 bp fragment containing only the putative insulator, were also cloned in the sense (d, f) and the antisense (e, g) orientations. Cos7 cells were transfected with these vectors and measured for the luciferase activities. Gray and black lines represent the vector backbone and cloned fragments, respectively. Red and blue boxes represent the putative <i>CCNB1IP1</i> insulator (260 bp) and enhancer (66bp), respectively. Luciferase activities relative to that of the control vector (a) are shown (mean ± sd, n = 3).</p>", "links"=>[], "tags"=>["mitotic cell cycle", "cyclin B 1", "JF", "Ccnb 1ip", "1.8 kbp segment", "Cyclin B 1 Interacting Protein 1 Gene Locus", "chromosomal domain levels", "barrier activity", "gene", "dna", "Ccnb 1ip enhancer", "C 57BL strain", "Mammalian Species Insulators", "Ccnb 1ip locus", "mouse Ccnb 1ip", "colony formation assays", "Ccnb 1ip insulator", "E 9.5 embryos"], "article_id"=>1463560, "categories"=>["Uncategorised"], "users"=>["Wataru Yoshida", "Junko Tomikawa", "Makoto Inaki", "Hiroshi Kimura", "Masafumi Onodera", "Kenichiro Hata", "Kazuhiko Nakabayashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0131204.g005", "stats"=>{"downloads"=>3, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Luciferase_reporter_assays_to_evaluate_of_the_enhancer_blocking_activity_of_the_human_putative_CCNB1IP1_insulator_/1463560", "title"=>"Luciferase reporter assays to evaluate of the enhancer-blocking activity of the human putative <i>CCNB1IP1</i> insulator.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 02:46:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/2148681"], "description"=>"<p>The <i>Ccnb1ip1</i> insulator or the cHS4 insulator was cloned at both sides of the neomycin-resistant gene (PGK-neo). Red and purple boxes represent the <i>Ccnb1ip1</i> insulator, and cHS4 insulator, respectively. Cos7 cells were transfected with these vectors in triplicates. The average numbers of the colonies formed without G418 selection are 86, 72, and 82, for PGK-neo alone, PGK-neo with <i>Ccnb1ip1</i> insulators, and PGK-neo with cHS4 insulators, respectively. The average numbers of the colonies formed with G418 selection are 9, 14, and 24, for PGK-neo alone, PGK-neo with <i>Ccnb1ip1</i> insulators, and PGK-neo with cHS4 insulators, respectively. Percentage numbers of the G418-resistant colonies relative to that for PGK-neo alone are shown for PGK-neo with <i>Ccnb1ip1</i> insulators and PGK-neo with cHS4 insulators (mean ± sd, n = 3).</p>", "links"=>[], "tags"=>["mitotic cell cycle", "cyclin B 1", "JF", "Ccnb 1ip", "1.8 kbp segment", "Cyclin B 1 Interacting Protein 1 Gene Locus", "chromosomal domain levels", "barrier activity", "gene", "dna", "Ccnb 1ip enhancer", "C 57BL strain", "Mammalian Species Insulators", "Ccnb 1ip locus", "mouse Ccnb 1ip", "colony formation assays", "Ccnb 1ip insulator", "E 9.5 embryos"], "article_id"=>1463558, "categories"=>["Uncategorised"], "users"=>["Wataru Yoshida", "Junko Tomikawa", "Makoto Inaki", "Hiroshi Kimura", "Masafumi Onodera", "Kenichiro Hata", "Kazuhiko Nakabayashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0131204.g003", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Colony_formation_assays_to_evaluate_the_barrier_activity_of_the_Ccnb1ip1_insulator_/1463558", "title"=>"Colony formation assays to evaluate the barrier activity of the <i>Ccnb1ip1</i> insulator.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 02:46:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/2148680"], "description"=>"<p>(A) Identification of the <i>Ccnb1ip1</i> insulator and enhancer in the 1.8 kbp fragment. DNA fragments and their orientations cloned immediately upstream of luc2 in the pGL4.23 [luc2/minP] vector (a) were: 1.8kbp fragment in the sense orientation (b) and in the antisense orientation (c), 464-bp (nt.886 to nt.1349) fragment in the sense (d) and the antisense (e) orientations, 185-bp (nt.1128 to nt.1312) fragment in the sense (f) and the antisense (g) orientations, and 242-bp (nt.886 to nt.1127) fragment in the sense (h) and the antisense (i) orientations. Cos7 cells were transfected with these vectors and measured for the luciferase activities. Gray and black lines represent the vector backbone and cloned fragments, respectively. Red and blue boxes represent the 242 bp insulator and the 185 bp enhancer, respectively. Luciferase activities relative to that of the control vector (a) are shown (mean ± sd, n = 3). (B) Enhancer-blocking activity of the <i>Ccnb1ip1</i> insulator against the SV40 enhancer. Red, purple, and black boxes represent the <i>Ccnb1ip1</i> insulator, cHS4 insulator, and SV40 enhancer, respectively. DNA elements cloned upstream of luc2 in the pGL4.23 vector (a) were: SV40 enhancer (b), SV40 enhancer and <i>Ccnb1ip1</i> insulator in order of enhancer, insulator, and minimal promoter (c) and in order of insulator, enhancer, and minimal promoter (d), SV40 enhancer and cHS4 insulator in order of enhancer, insulator, and minimal promoter (e) and in order of insulator, enhancer, and minimal promoter (f). Luciferase activities relative to that of the control vector (a) are shown (mean ± sd, n = 3).</p>", "links"=>[], "tags"=>["mitotic cell cycle", "cyclin B 1", "JF", "Ccnb 1ip", "1.8 kbp segment", "Cyclin B 1 Interacting Protein 1 Gene Locus", "chromosomal domain levels", "barrier activity", "gene", "dna", "Ccnb 1ip enhancer", "C 57BL strain", "Mammalian Species Insulators", "Ccnb 1ip locus", "mouse Ccnb 1ip", "colony formation assays", "Ccnb 1ip insulator", "E 9.5 embryos"], "article_id"=>1463557, "categories"=>["Uncategorised"], "users"=>["Wataru Yoshida", "Junko Tomikawa", "Makoto Inaki", "Hiroshi Kimura", "Masafumi Onodera", "Kenichiro Hata", "Kazuhiko Nakabayashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0131204.g002", "stats"=>{"downloads"=>3, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Luciferase_reporter_assays_to_evaluate_the_enhancer_blocking_activity_of_the_Ccnb1ip1_insulator_/1463557", "title"=>"Luciferase reporter assays to evaluate the enhancer-blocking activity of the <i>Ccnb1ip1</i> insulator.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 02:46:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/2148679"], "description"=>"<p>(A) A schematic map of the <i>Ccnb1ip1</i>-<i>Parp2</i> locus. The 1.8 kbp segment is located between the <i>Parp2</i> and <i>Ccnb1ip1</i> genes. Individual CpG sites are shown as vertical bars. Horizontal bars (numbered from 1 to 7) indicate the genomic regions whose DNA methylation levels were assessed by bisulfite sequencing. (B) DNA methylation statuses of the genomic regions #1 to #7 shown in Fig 1A in E9.5 embryos of C57BL/6 (top) and JF1 (bottom). Each black bar shows the DNA methylation level (0 to 100%) at an individual CpG site. Gray bars indicate CpG sites present in the B6 strain but absent in the JF1 strain due to DNA polymorphism. Sequence analysis revealed that the 220bp region at the right end of the 1.8kbp segment was present in the B6 genome in an inverted orientation. This 220bp interval is boxed: Region 2 in C57BL/6 and part of Region 3 in JF1.</p>", "links"=>[], "tags"=>["mitotic cell cycle", "cyclin B 1", "JF", "Ccnb 1ip", "1.8 kbp segment", "Cyclin B 1 Interacting Protein 1 Gene Locus", "chromosomal domain levels", "barrier activity", "gene", "dna", "Ccnb 1ip enhancer", "C 57BL strain", "Mammalian Species Insulators", "Ccnb 1ip locus", "mouse Ccnb 1ip", "colony formation assays", "Ccnb 1ip insulator", "E 9.5 embryos"], "article_id"=>1463556, "categories"=>["Uncategorised"], "users"=>["Wataru Yoshida", "Junko Tomikawa", "Makoto Inaki", "Hiroshi Kimura", "Masafumi Onodera", "Kenichiro Hata", "Kazuhiko Nakabayashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0131204.g001", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_DNA_methylation_boundary_identified_in_the_1_8_kbp_segment_that_is_present_in_the_JF1_genome_but_absent_in_the_B6_genome_/1463556", "title"=>"The DNA methylation boundary identified in the 1.8 kbp segment that is present in the JF1 genome but absent in the B6 genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 02:46:43"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"7", "full-text"=>"2", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}

Relative Metric

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