Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses", "type"=>"journal", "authors"=>[{"first_name"=>"Jumpei", "last_name"=>"Ito", "scopus_author_id"=>"55898709600"}, {"first_name"=>"Ryota", "last_name"=>"Sugimoto", "scopus_author_id"=>"57195263402"}, {"first_name"=>"Hirofumi", "last_name"=>"Nakaoka", "scopus_author_id"=>"57195433372"}, {"first_name"=>"Shiro", "last_name"=>"Yamada", "scopus_author_id"=>"57194636298"}, {"first_name"=>"Tetsuaki", "last_name"=>"Kimura", "scopus_author_id"=>"26643384000"}, {"first_name"=>"Takahide", "last_name"=>"Hayano", "scopus_author_id"=>"56437405500"}, {"first_name"=>"Ituro", "last_name"=>"Inoue", "scopus_author_id"=>"55119019400"}], "year"=>2017, "source"=>"PLoS Genetics", "identifiers"=>{"doi"=>"10.1371/journal.pgen.1006883", "sgr"=>"85026679533", "pui"=>"617638871", "scopus"=>"2-s2.0-85026679533", "issn"=>"15537404", "pmid"=>"28700586", "isbn"=>"1111111111"}, "id"=>"0a8f6087-ed93-35bd-a57f-340c6615179c", "abstract"=>"Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified \"HERV/LTR-shared regulatory element (HSRE),\" defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG), embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2), hematopoietic TFs (e.g., SPI1 (PU1), GATA1/2, and TAL1), and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (http://herv-tfbs.com/). This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into the transcriptional modulation systems of HERV/LTRs and ancestral HERVs.", "link"=>"http://www.mendeley.com/research/systematic-identification-characterization-regulatory-elements-derived-human-endogenous-retroviruses", "reader_count"=>21, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85026679533"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85026679533?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85026679533&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=85026679533&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/85026679533", "dc:identifier"=>"SCOPUS_ID:85026679533", "eid"=>"2-s2.0-85026679533", "dc:title"=>"Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses", "dc:creator"=>"Ito J.", "prism:publicationName"=>"PLoS Genetics", "prism:issn"=>"15537390", "prism:eIssn"=>"15537404", "prism:volume"=>"13", "prism:issueIdentifier"=>"7", "prism:pageRange"=>nil, "prism:coverDate"=>"2017-07-01", "prism:coverDisplayDate"=>"July 2017", "prism:doi"=>"10.1371/journal.pgen.1006883", "citedby-count"=>"5", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"National Institute of Genetics Mishima", "affiliation-city"=>"Mishima", "affiliation-country"=>"Japan"}, {"@_fa"=>"true", "affilname"=>"Sokendai Graduate University for Advanced Studies", "affiliation-city"=>"Hayama", "affiliation-country"=>"Japan"}], "pubmed-id"=>"28700586", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e1006883", "source-id"=>"4000151808", "openaccess"=>"1", "openaccessFlag"=>true}

Twitter

Counter

  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"240", "xml_views"=>"11", "html_views"=>"1249"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"143", "xml_views"=>"0", "html_views"=>"325"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"58", "xml_views"=>"8", "html_views"=>"134"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"48", "xml_views"=>"0", "html_views"=>"151"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"50", "xml_views"=>"1", "html_views"=>"130"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"27", "xml_views"=>"0", "html_views"=>"85"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"52", "xml_views"=>"0", "html_views"=>"85"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"46", "xml_views"=>"0", "html_views"=>"43"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"32", "xml_views"=>"0", "html_views"=>"57"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"41", "xml_views"=>"3", "html_views"=>"78"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"32", "xml_views"=>"5", "html_views"=>"51"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"29", "xml_views"=>"7", "html_views"=>"69"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"25", "xml_views"=>"4", "html_views"=>"64"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"28", "xml_views"=>"5", "html_views"=>"60"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"19", "xml_views"=>"1", "html_views"=>"37"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"28", "xml_views"=>"0", "html_views"=>"82"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"19", "xml_views"=>"1", "html_views"=>"38"}

PMC Usage Stats

  • {"unique-ip"=>"44", "full-text"=>"37", "pdf"=>"22", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"15", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"51", "full-text"=>"46", "pdf"=>"17", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"56", "full-text"=>"25", "pdf"=>"10", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"25", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"32", "full-text"=>"35", "pdf"=>"16", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"8", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"22", "full-text"=>"23", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"22", "full-text"=>"26", "pdf"=>"15", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"2"}
  • {"unique-ip"=>"22", "full-text"=>"22", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
Loading … Spinner
There are currently no alerts