Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
Publication Date
December 09, 2010
Journal
PLOS Genetics
Authors
Joseph K. Pickrell, Athma A. Pai, Yoav Gilad & Jonathan K. Pritchard
Volume
6
Issue
12
Pages
e1001236
DOI
https://dx.plos.org/10.1371/journal.pgen.1001236
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1001236
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21151575
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000347
Europe PMC
http://europepmc.org/abstract/MED/21151575
Web of Science
000285578900014
Scopus
78650689920
Mendeley
http://www.mendeley.com/research/noisy-splicing-drives-mrna-isoform-diversity-human-cells
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Noisy splicing drives mRNA isoform diversity in human cells", "type"=>"journal", "authors"=>[{"first_name"=>"Joseph K.", "last_name"=>"Pickrell", "scopus_author_id"=>"26634283400"}, {"first_name"=>"Athma A.", "last_name"=>"Pai", "scopus_author_id"=>"35366984200"}, {"first_name"=>"Yoav", "last_name"=>"Gilad", "scopus_author_id"=>"6602166624"}, {"first_name"=>"Jonathan K.", "last_name"=>"Pritchard", "scopus_author_id"=>"57200979225"}], "year"=>2010, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-78650689920", "doi"=>"10.1371/journal.pgen.1001236", "sgr"=>"78650689920", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"21151575", "issn"=>"15537390", "pui"=>"361011551"}, "id"=>"5a9032d4-3ae8-37a7-9afb-3836723235ea", "abstract"=>"While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant. In this study, we examine the extent of alternative splicing in human cells using deep RNA sequencing and de novo identification of splice junctions. We demonstrate the existence of a large class of low abundance isoforms, encompassing approximately 150,000 previously unannotated splice junctions in our data. Newly-identified splice sites show little evidence of evolutionary conservation, suggesting that the majority are due to erroneous splice site choice. We show that sequence motifs involved in the recognition of exons are enriched in the vicinity of unconserved splice sites. We estimate that the average intron has a splicing error rate of approximately 0.7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution.", "link"=>"http://www.mendeley.com/research/noisy-splicing-drives-mrna-isoform-diversity-human-cells", "reader_count"=>294, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>21, "Researcher"=>92, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>105, "Student > Postgraduate"=>5, "Student > Master"=>17, "Other"=>12, "Student > Bachelor"=>16, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>21, "Researcher"=>92, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>105, "Student > Postgraduate"=>5, "Student > Master"=>17, "Other"=>12, "Student > Bachelor"=>16, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Agricultural and Biological Sciences"=>208, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>15, "Earth and Planetary Sciences"=>1, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>41, "Mathematics"=>2, "Medicine and Dentistry"=>11, "Neuroscience"=>2, "Sports and Recreations"=>1, "Physics and Astronomy"=>3, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>11}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>208}, "Computer Science"=>{"Computer Science"=>15}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>41}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Hong Kong"=>1, "United States"=>23, "Japan"=>1, "United Kingdom"=>8, "Switzerland"=>1, "Spain"=>2, "Canada"=>3, "Sweden"=>4, "Austria"=>1, "South Korea"=>1, "Netherlands"=>2, "Norway"=>1, "Brazil"=>1, "Italy"=>3, "Germany"=>2}, "group_count"=>16}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/813383"], "description"=>"<p>We divided all introns that are bounded by highly conserved splice sites into 100 bins based on length. We then calculated, in each bin, the mean fraction of sequencing reads from either splice site to an unconserved splice site. Plotted is this mean against the of the mean intron length (in base pairs) of introns in the bin. In red is a spline fit to these points.</p>", "links"=>[], "tags"=>["correlates", "intron"], "article_id"=>483753, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001236.g004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Splicing_error_rate_correlates_with_intron_length_/483753", "title"=>"Splicing error rate correlates with intron length.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-09 01:02:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/813508"], "description"=>"<p>As described in the main text, we split the observed junctions into five classes based on gene model databases. For each class, we present the number of such junctions, the average number of reads spanning each junction in that class, the percentage of the junctions observed in any tissue assayed in Wang et al. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001236#pgen.1001236-lWang1\" target=\"_blank\">[2]</a>, the percentage of 5′ and 3′ splice sites of each junction that fall near an annotated splice site (“near” here is defined as within 50 base pairs), and the percentage of the 5′ and 3′ splice sites of each junction that show strong evidence of evolutionary conservation (defined as a mean <i>phyloP</i> score <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001236#pgen.1001236-Pollard1\" target=\"_blank\">[31]</a> at the two canonical bases of the splice site).</p>", "links"=>[], "tags"=>["observed"], "article_id"=>483880, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001236.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_observed_junctions_/483880", "title"=>"Characteristics of observed junctions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-09 01:04:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/405685", "https://ndownloader.figshare.com/files/405687", "https://ndownloader.figshare.com/files/405694", "https://ndownloader.figshare.com/files/405700", "https://ndownloader.figshare.com/files/405709", "https://ndownloader.figshare.com/files/405713", "https://ndownloader.figshare.com/files/405724", "https://ndownloader.figshare.com/files/405732", "https://ndownloader.figshare.com/files/405733"], "description"=>"<div><p>While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant. In this study, we examine the extent of alternative splicing in human cells using deep RNA sequencing and <em>de novo</em> identification of splice junctions. We demonstrate the existence of a large class of low abundance isoforms, encompassing approximately 150,000 previously unannotated splice junctions in our data. Newly-identified splice sites show little evidence of evolutionary conservation, suggesting that the majority are due to erroneous splice site choice. We show that sequence motifs involved in the recognition of exons are enriched in the vicinity of unconserved splice sites. We estimate that the average intron has a splicing error rate of approximately 0.7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution.</p></div>", "links"=>[], "tags"=>["noisy", "splicing", "drives", "mrna", "isoform", "cells"], "article_id"=>140163, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001236.s001", "https://dx.doi.org/10.1371/journal.pgen.1001236.s002", "https://dx.doi.org/10.1371/journal.pgen.1001236.s003", "https://dx.doi.org/10.1371/journal.pgen.1001236.s004", "https://dx.doi.org/10.1371/journal.pgen.1001236.s005", "https://dx.doi.org/10.1371/journal.pgen.1001236.s006", "https://dx.doi.org/10.1371/journal.pgen.1001236.s007", "https://dx.doi.org/10.1371/journal.pgen.1001236.s008", "https://dx.doi.org/10.1371/journal.pgen.1001236.s009"], "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Noisy_Splicing_Drives_mRNA_Isoform_Diversity_in_Human_Cells/140163", "title"=>"Noisy Splicing Drives mRNA Isoform Diversity in Human Cells", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-12-09 00:02:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/813458"], "description"=>"<p>A. Plotted is the enrichment of all possible hexamers exonic of either 5′ or 3′ noise splice sites. In light blue are hexamers identified as exonic splicing enhancers by Fairbrother et al. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001236#pgen.1001236-Fairbrother1\" target=\"_blank\">[35]</a>, and in dark blue are hexamers that are good matches to the consensus U1 snSNP binding site (we include all hexamers matching five contiguous bases of “AGGTAAG”). B and C. Hexamers from A. mark borders of constitutively spliced exons. Each point is the fraction of hexamers starting at that position relative to a constitutively spliced exon (in these cells) which match the hexamers identified as significantly enriched exonic or intronic of the “noise” 5′ or 3′ splice sites.</p>", "links"=>[], "tags"=>["enriched", "unconserved", "splice", "sites", "exon"], "article_id"=>483824, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001236.g005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hexamers_enriched_near_unconserved_splice_sites_are_relevant_in_exon_definition_/483824", "title"=>"Hexamers enriched near unconserved splice sites are relevant in exon definition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-09 01:03:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/813179"], "description"=>"<p>In the top panel, we plot the average expression level at each base in a region surrounding <i>HERPUD1</i>. In blue are bases annotated as exonic, and in black are those annotated as not exonic. In the middle panel, we plot the positions of all splice junctions in the region identified in our data. In black are splice junctions that are present in gene databases; in red are those that are not. The number of sequencing reads supporting each junction is written to the right of each junction, and junctions are ordered from top to bottom of the plot according to their coverage. In the bottom panel, we show the gene models in the region from Ensembl. The blue boxes show the positions of exons, and the black lines the positions of introns.</p>", "links"=>[], "tags"=>["splice", "junctions"], "article_id"=>483549, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001236.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_splice_junctions_identified_in_a_gene_/483549", "title"=>"An example of splice junctions identified in a gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-09 00:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/813322"], "description"=>"<p>In each panel, we plot the mean <i>phyloP</i> score <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001236#pgen.1001236-Pollard1\" target=\"_blank\">[31]</a> at each base surrounding the splice site. In the top panels are annotated splice sites, and in the bottom panels are unannotated splice sites. In blue are bases exonic of the splice site, and in black are those intronic of the splice site, as diagrammed below each panel.</p>", "links"=>[], "tags"=>["splice", "junctions", "evolutionary"], "article_id"=>483691, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001236.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unannotated_splice_junctions_show_little_evidence_of_evolutionary_conservation_/483691", "title"=>"Unannotated splice junctions show little evidence of evolutionary conservation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-09 01:01:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/813080"], "description"=>"<p>A. We plot, as a function of number of supporting reads, the fraction of junctions 1) matching GT-AG, the splice site consensus sequences (black), 2) matching a control pair of dinucleotides (grey), 3) annotated in EST databases (light blue), or 4) annotated in gene databases (dark blue). B. We split all junctions into those that are annotated in gene model databases and those that are not. Plotted is the cumulative number of junctions of each type by expression level. Unannotated junctions are expressed at much lower levels than annotated junctions. C and D. Alternative splice junctions near known protein-coding junctions show a periodic pattern. At each alternatively-spliced protein-coding 3′ or 5′ splice site, we counted the positions of AG (or GT, respectively) dinucleotides used as alternative splice sites, then averaged this across splice sites (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001236#s4\" target=\"_blank\">Methods</a>). The red points denote positions that are a multiple of three base pairs from the major splice form, and the black points those that are not. The blue box below each panel shows the position of the exon.</p>", "links"=>[], "tags"=>["unannotated", "splicing"], "article_id"=>483447, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Joseph K. Pickrell", "Athma A. Pai", "Yoav Gilad", "Jonathan K. Pritchard"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001236.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extensive_unannotated_splicing_in_human_cells_/483447", "title"=>"Extensive unannotated splicing in human cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-09 00:57:27"}

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Relative Metric

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