Transposable Elements Re-Wire and Fine-Tune the Transcriptome
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{"title"=>"Transposable Elements Re-Wire and Fine-Tune the Transcriptome", "type"=>"generic", "authors"=>[{"first_name"=>"Michael", "last_name"=>"Cowley", "scopus_author_id"=>"7006376748"}, {"first_name"=>"Rebecca J.", "last_name"=>"Oakey", "scopus_author_id"=>"7007157254"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84873507928", "sgr"=>"84873507928", "issn"=>"15537390", "doi"=>"10.1371/journal.pgen.1003234", "pmid"=>"23358118", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pui"=>"368295325"}, "id"=>"9cf5de4b-7450-37ec-a9bf-6b5fe0371804", "abstract"=>"What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs-particularly retrotransposons-contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.", "link"=>"http://www.mendeley.com/research/transposable-elements-rewire-finetune-transcriptome", "reader_count"=>304, "reader_count_by_academic_status"=>{"Unspecified"=>10, "Professor > Associate Professor"=>19, "Librarian"=>2, "Researcher"=>80, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>82, "Student > Postgraduate"=>8, "Student > Master"=>38, "Other"=>10, "Student > Bachelor"=>24, "Lecturer"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>10, "Professor > Associate Professor"=>19, "Librarian"=>2, "Researcher"=>80, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>82, "Student > Postgraduate"=>8, "Student > Master"=>38, "Other"=>10, "Student > Bachelor"=>24, "Lecturer"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>15, "Agricultural and Biological Sciences"=>215, "Philosophy"=>1, "Chemistry"=>1, "Computer Science"=>5, "Economics, Econometrics and Finance"=>1, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>45, "Medicine and Dentistry"=>8, "Neuroscience"=>3, "Psychology"=>4, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Psychology"=>{"Psychology"=>4}, "Unspecified"=>{"Unspecified"=>15}, "Environmental Science"=>{"Environmental Science"=>1}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>3}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>215}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>45}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"United States"=>4, "Japan"=>1, "Egypt"=>1, "United Kingdom"=>2, "Portugal"=>3, "Spain"=>3, "New Zealand"=>1, "Canada"=>3, "Netherlands"=>3, "Sweden"=>1, "Taiwan"=>1, "Brazil"=>5, "Mexico"=>1, "France"=>3, "Germany"=>5}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/500460"], "description"=>"<p>Impacts on the transcriptome may be considered transcriptional (or co-transcriptional) and posttranscriptional. The former mechanisms include insertion of a TE into an ORF; provision of an alternative promoter that may be tissue- or stage-specific in its activity; promotion of alternative splicing either through prevention of the splicing machinery from recognising a splice acceptor site in an endogenous exon (exon skipping) or through incorporation of the TE into the mature transcript (exonization); promotion of alternative polyadenylation (poly(A)) either by providing an alternative polyadenylation signal or by promoter activity interfering with host gene transcription and causing upstream polyadenylation; and by introducing transcription factor binding sites that may confer tissue- or stage-specific expression, or link a gene into a transcriptional network. Posttranscriptional regulation involves TE-derived small RNAs binding to host transcripts. In the case of <i>Drosophila Nanos</i> transcripts, small RNAs destabilise the transcript by recruiting the deadenylation machinery. In the case of murine <i>Rasgrf1</i>, the binding of small RNAs to an ncRNA associated with one allele results in the recruitment of the de novo methylation machinery to that allele, causing allele-specific <i>Rasgrf1</i> expression. The events occurring downstream of small RNA binding are therefore diverse and locus-specific.</p>", "links"=>[], "tags"=>["mobilome"], "article_id"=>170989, "categories"=>["Genetics", "Developmental Biology", "Evolutionary Biology"], "users"=>["Michael Cowley", "Rebecca J. Oakey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003234.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_How_the_mobilome_can_impact_the_transcriptome_/170989", "title"=>"How the mobilome can impact the transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 16:25:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/500534"], "description"=>"<p>(A) Schematic of the 3′ end of the human <i>ATRN</i> gene. An L1 element (black bar) inserted between exons 24 and 26 (numbered boxes) provides a terminal exon, translation termination site (red arrowhead), and polyadenylation signal (arrow) for a subset of transcripts. Alternative splicing produces an mRNA isoform that is polyadenylated in exon 30; only this isoform encodes transmembrane and cytoplasmic domains. Dashed lines, splicing event. (B) Inheritance of DNA methylation at the imprinted <i>Mcts2</i> and <i>Rasgrf1</i> genes in mouse. The promoter of <i>Mcts2</i> is methylated (filled lollipops) in the oocyte and unmethylated (empty lollipops) in sperm. This is opposite to the <i>Rasgrf1</i> promoter. After fertilisation, these differences persist, marking the origin of the parental alleles even in terminally differentiated cell types, where the unmethylated promoters are transcriptionally active (arrows). (C) Relationship between the retrogene <i>Mcts2</i> and the gene <i>H13</i>. (Top) Locus structure. <i>Mcts2</i> (green box) is situated between exons 4 and 5 of <i>H13</i>. Allele-specific differences in methylation at the <i>Mcts2</i> promoter result in expression of <i>Mcts2</i> from the paternal allele only. The <i>H13</i> promoter is unmethylated and active on both alleles. <i>H13</i> transcripts use alternative polyadenylation sites (vertical blue arrows). Vertical green arrow, single <i>Mcts2</i> polyadenylation site. (Middle) Representative transcript produced from transcription of the maternal allele. <i>H13</i> transcripts splice around <i>Mcts2</i> and use one of three downstream polyadenylation signals (one transcript is shown for clarity). (Bottom) Representative transcripts produced from transcription of the paternal allele. <i>Mcts2</i> is transcribed and the mRNA is polyadenylated (AAA). <i>H13</i> transcripts use one of two upstream polyadenylation signals (one transcript is shown for clarity). Transcription of the retrogene <i>Mcts2</i> is associated with upstream polyadenylation of <i>H13</i> transcripts.</p>", "links"=>[], "tags"=>["mrna"], "article_id"=>171060, "categories"=>["Genetics", "Developmental Biology", "Evolutionary Biology"], "users"=>["Michael Cowley", "Rebecca J. Oakey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003234.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Retrotransposition_can_influence_mRNA_processing_/171060", "title"=>"Retrotransposition can influence mRNA processing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 16:26:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/500412"], "description"=>"<p>Active human retrotransposons.</p>", "links"=>[], "tags"=>["genetics and genomics", "developmental biology", "Evolutionary biology"], "article_id"=>170938, "categories"=>["Genetics", "Developmental Biology", "Evolutionary Biology"], "users"=>["Michael Cowley", "Rebecca J. Oakey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003234.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Active_human_retrotransposons_/170938", "title"=>"Active human retrotransposons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 16:25:26"}

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  • {"unique-ip"=>"20", "full-text"=>"18", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"21", "supp-data"=>"0", "cited-by"=>"3", "year"=>"2017", "month"=>"8"}
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  • {"unique-ip"=>"11", "full-text"=>"13", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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  • {"unique-ip"=>"24", "full-text"=>"22", "pdf"=>"12", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"12", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
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  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"25", "full-text"=>"19", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"15", "full-text"=>"12", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"32", "full-text"=>"39", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"26", "full-text"=>"27", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"19", "full-text"=>"16", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[272, 472, 600, 713, 815, 911, 1004, 1094, 1185, 1273, 1358, 1441]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}]}

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