Canonical A-to-I and C-to-U RNA Editing Is Enriched at 3′UTRs and microRNA Target Sites in Multiple Mouse Tissues
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{"title"=>"Canonical A-to-I and C-to-U RNA editing is enriched at 3′UTRs and microrna target sites in multiple mouse tissues", "type"=>"journal", "authors"=>[{"first_name"=>"Tongjun", "last_name"=>"Gu", "scopus_author_id"=>"55114229800"}, {"first_name"=>"Frank W.", "last_name"=>"Buaas", "scopus_author_id"=>"6508233490"}, {"first_name"=>"Allen K.", "last_name"=>"Simons", "scopus_author_id"=>"55117756700"}, {"first_name"=>"Cheryl L.", "last_name"=>"Ackert-Bicknell", "scopus_author_id"=>"57195224283"}, {"first_name"=>"Robert E.", "last_name"=>"Braun", "scopus_author_id"=>"56347372800"}, {"first_name"=>"Matthew A.", "last_name"=>"Hibbs", "scopus_author_id"=>"8878818400"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"364479993", "sgr"=>"84858682499", "issn"=>"19326203", "pmid"=>"22448268", "scopus"=>"2-s2.0-84858682499", "doi"=>"10.1371/journal.pone.0033720", "isbn"=>"1932-6203"}, "id"=>"8912d4e4-8ca4-35a9-b6c0-5bf4daae5ea2", "abstract"=>"RNA editing is a process that modifies RNA nucleotides and changes the efficiency and fidelity of the central dogma. Enzymes that catalyze RNA editing are required for life, and defects in RNA editing are associated with many diseases. Recent advances in sequencing have enabled the genome-wide identification of RNA editing sites in mammalian transcriptomes. Here, we demonstrate that canonical RNA editing (A-to-I and C-to-U) occurs in liver, white adipose, and bone tissues of the laboratory mouse, and we show that apparent non-canonical editing (all other possible base substitutions) is an artifact of current high-throughput sequencing technology. Further, we report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 3' UTRs, specifically at microRNA target sites, suggesting both regulatory and functional consequences for RNA editing", "link"=>"http://www.mendeley.com/research/canonical-atoi-ctou-rna-editing-enriched-3utrs-microrna-target-sites-multiple-mouse-tissues", "reader_count"=>62, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Researcher"=>22, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>6, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Researcher"=>22, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>6, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>47, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>4, "Germany"=>1, "India"=>1}, "group_count"=>2}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/665204"], "description"=>"<p>A) Distribution of RNA editing types with and without a filter for significant strand bias from RNA-seq data. B,C) RNA-seq traces are shown for one canonical RNA editing site (C-to-U in <i>Serinc1</i>) and for one non-canonical editing site (G-to-C in <i>Lars2</i>). Reads sequenced in the sense direction are shown in dark grey, while reads sequenced in the reverse direction are shown in light grey. D,E) Sanger sequencing validation results for sites in <i>Serinc1</i> and <i>Lars2</i>. F,G) RFLP validation of sites in <i>Serinc1</i> and <i>Lars2</i>. Samples exposed to enzyme are labeled “en+” and control samples are labeled “en-.” H) Genomic distribution of editing sites and random background.</p>", "links"=>[], "tags"=>["validation", "editing", "sites", "observed", "rna-seq"], "article_id"=>335685, "categories"=>["Biological Sciences", "Biochemistry", "Genetics"], "users"=>["Tongjun Gu", "Frank W. Buaas", "Allen K. Simons", "Cheryl L. Ackert-Bicknell", "Robert E. Braun", "Matthew A. Hibbs"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033720.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_and_validation_of_editing_sites_observed_in_RNA_seq_data_/335685", "title"=>"Distribution and validation of editing sites observed in RNA-seq data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:34:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/665290"], "description"=>"<p>A) Distribution of editing ratio for all observed canonical and non-canonical RNA editing sites in our adipose RNA-seq data shows that the ratio is higher for non-canonical than canonical sites. B) Distribution of Fisher's exact test p-values for strand bias. Non-canonical RNA editing sites shows an extreme peak around zero, indicating that most non-canonical RNA editing sites are supported by strand biased reads. C) Overview of our RNA editing analysis pipeline.</p>", "links"=>[], "tags"=>["high-confidence", "rna", "editing"], "article_id"=>335777, "categories"=>["Biological Sciences", "Biochemistry", "Genetics"], "users"=>["Tongjun Gu", "Frank W. Buaas", "Allen K. Simons", "Cheryl L. Ackert-Bicknell", "Robert E. Braun", "Matthew A. Hibbs"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033720.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_high_confidence_RNA_editing_sites_/335777", "title"=>"Identification of high-confidence RNA editing sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:36:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/665407"], "description"=>"<p>One hundred nucleotides of the 3′UTR of <i>Rpa1</i> is shown. Multiple microRNA target sites form a dense cluster in this region and contain many A-to-I editing sites. Red bases represent RNA editing sites, and blue and green bases represent different microRNA seed locations.</p>", "links"=>[], "tags"=>["rna", "editing", "microrna"], "article_id"=>335891, "categories"=>["Biological Sciences", "Biochemistry", "Genetics"], "users"=>["Tongjun Gu", "Frank W. Buaas", "Allen K. Simons", "Cheryl L. Ackert-Bicknell", "Robert E. Braun", "Matthew A. Hibbs"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033720.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_RNA_editing_at_microRNA_target_sites_/335891", "title"=>"Example of RNA editing at microRNA target sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:38:11"}

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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"10", "full-text"=>"9", "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"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[316, 541, 663, 766, 856, 950, 1041, 1128, 1218, 1302, 1382, 1456, 1526, 1593, 1657, 1729, 1796, 1862, 1930, 1999, 2065, 2132, 2202, 2261, 2319]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[333, 576, 707, 814, 908, 1004, 1104, 1197, 1280, 1370, 1449, 1531, 1603, 1673, 1742, 1817, 1886, 1954, 2025, 2098, 2171, 2234, 2304, 2365, 2431]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[324, 551, 679, 782, 879, 971, 1064, 1154, 1245, 1328, 1406, 1476, 1541, 1617, 1683, 1754, 1818, 1893, 1962, 2025, 2092, 2164, 2227, 2294, 2355]}]}
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