NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulator...
Gespeichert in:
| Veröffentlicht in: | PloS one 2017-04, Vol.12 (4), p.e0174798-e0174798 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0174798 |
|---|---|
| container_issue | 4 |
| container_start_page | e0174798 |
| container_title | PloS one |
| container_volume | 12 |
| creator | Hsu, Min-Kung Lin, Hsuan-Yu Chen, Feng-Chi |
| description | Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms. |
| doi_str_mv | 10.1371/journal.pone.0174798 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1883824932</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A488304404</galeid><doaj_id>oai_doaj_org_article_970c506864e640caa8080a2e75c656e2</doaj_id><sourcerecordid>A488304404</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-8d0113c3661db713f170e94d670650945c69a77c21f30f9bc267f5f66f1219563</originalsourceid><addsrcrecordid>eNqNk11v0zAUhiMEYmPwDxBEQkJw0WLHju3sAqkqX5UGk_i6Na5z3Lpy42InE_33OGs2NWgXKJHi2M957fP6nCx7itEUE47fbHwXGuWmO9_AFGFOeSXuZae4IsWEFYjcPxqfZI9i3CBUEsHYw-ykEIRVSNDT7NeXz-_yuVMxWmMhnOezPICzaukgV02dx31sYataq3M9UDr9-SZvvXe58SFvfBMhvZMt1Fa1UOc1aLXP4QqaNj7OHhjlIjwZvmfZjw_vv88_TS4uPy7ms4uJZlXRTkSNMCaaMIbrJcfEYI6gojXjiJWoomXCFOe6wIYgUy11wbgpDWMGF7gqGTnLnh90d85HOZgTJRaCiIImIxKxOBC1Vxu5C3arwl56ZeX1hA8rqUJK1IGsONIlYoJRYBRppQQSSBXA0zFKBr3W22G3bpnS1inToNxIdLzS2LVc-StZEp687wVeDQLB_-4gtnJrowbnVAO-uz43xaxMcEJf_IPend1ArVRKwDbGp311LypnNGGIUkQTNb2DSk8NW6tTJRmb5kcBr0cBiWnhT7tSXYxy8e3r_7OXP8fsyyN2Dcq16-hd15dWHIP0AOrgYwxgbk3GSPaNcOOG7BtBDo2Qwp4dX9Bt0E3lk7-oYQEa</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1883824932</pqid></control><display><type>article</type><title>NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><source>Public Library of Science (PLoS)</source><creator>Hsu, Min-Kung ; Lin, Hsuan-Yu ; Chen, Feng-Chi</creator><creatorcontrib>Hsu, Min-Kung ; Lin, Hsuan-Yu ; Chen, Feng-Chi</creatorcontrib><description>Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0174798</identifier><identifier>PMID: 28369084</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adenocarcinoma ; Adenocarcinoma - metabolism ; Adenocarcinoma of Lung ; Alignment ; Alternative Splicing ; Annotations ; Assembly ; Bacteria ; Biochemistry ; Biodegradation ; Bioinformatics ; Biological activity ; Biology and Life Sciences ; Blood ; Brain ; Cell differentiation ; Chromatin ; Classification ; Coding ; Codons ; Computer Simulation ; Conserved sequence ; Decay ; Degradation ; Dentistry ; Differentiation ; Dystrophy ; Effectors ; Eukaryotes ; Evolution ; Exons ; Gene expression ; Gene Expression Profiling - methods ; Gene regulation ; Genetics ; Genomes ; Genomics ; Health sciences ; Humans ; Internet ; Kinases ; Lung cancer ; Lung Neoplasms - metabolism ; Lungs ; Mammals ; Medical research ; Medicine and Health Sciences ; Messenger RNA ; Movement disorders ; Muscular dystrophy ; Mutation ; Neurodegenerative diseases ; Nonsense Mediated mRNA Decay ; Nucleotide sequence ; Nucleotides ; Parkinson's disease ; Placenta ; Protein kinase ; Proteins ; Quality control ; Retention ; Retinitis pigmentosa ; Ribonucleic acid ; RNA ; Simulation ; Single nucleotide polymorphisms ; Stop codon ; Surveillance ; Switching ; T cell receptors ; Technology ; Transcription ; Vertebrates</subject><ispartof>PloS one, 2017-04, Vol.12 (4), p.e0174798-e0174798</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Hsu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2017 Hsu et al 2017 Hsu et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-8d0113c3661db713f170e94d670650945c69a77c21f30f9bc267f5f66f1219563</citedby><cites>FETCH-LOGICAL-c692t-8d0113c3661db713f170e94d670650945c69a77c21f30f9bc267f5f66f1219563</cites><orcidid>0000-0002-1437-4420</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378362/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378362/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28369084$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hsu, Min-Kung</creatorcontrib><creatorcontrib>Lin, Hsuan-Yu</creatorcontrib><creatorcontrib>Chen, Feng-Chi</creatorcontrib><title>NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.</description><subject>Adenocarcinoma</subject><subject>Adenocarcinoma - metabolism</subject><subject>Adenocarcinoma of Lung</subject><subject>Alignment</subject><subject>Alternative Splicing</subject><subject>Annotations</subject><subject>Assembly</subject><subject>Bacteria</subject><subject>Biochemistry</subject><subject>Biodegradation</subject><subject>Bioinformatics</subject><subject>Biological activity</subject><subject>Biology and Life Sciences</subject><subject>Blood</subject><subject>Brain</subject><subject>Cell differentiation</subject><subject>Chromatin</subject><subject>Classification</subject><subject>Coding</subject><subject>Codons</subject><subject>Computer Simulation</subject><subject>Conserved sequence</subject><subject>Decay</subject><subject>Degradation</subject><subject>Dentistry</subject><subject>Differentiation</subject><subject>Dystrophy</subject><subject>Effectors</subject><subject>Eukaryotes</subject><subject>Evolution</subject><subject>Exons</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene regulation</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health sciences</subject><subject>Humans</subject><subject>Internet</subject><subject>Kinases</subject><subject>Lung cancer</subject><subject>Lung Neoplasms - metabolism</subject><subject>Lungs</subject><subject>Mammals</subject><subject>Medical research</subject><subject>Medicine and Health Sciences</subject><subject>Messenger RNA</subject><subject>Movement disorders</subject><subject>Muscular dystrophy</subject><subject>Mutation</subject><subject>Neurodegenerative diseases</subject><subject>Nonsense Mediated mRNA Decay</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Parkinson's disease</subject><subject>Placenta</subject><subject>Protein kinase</subject><subject>Proteins</subject><subject>Quality control</subject><subject>Retention</subject><subject>Retinitis pigmentosa</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Simulation</subject><subject>Single nucleotide polymorphisms</subject><subject>Stop codon</subject><subject>Surveillance</subject><subject>Switching</subject><subject>T cell receptors</subject><subject>Technology</subject><subject>Transcription</subject><subject>Vertebrates</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11v0zAUhiMEYmPwDxBEQkJw0WLHju3sAqkqX5UGk_i6Na5z3Lpy42InE_33OGs2NWgXKJHi2M957fP6nCx7itEUE47fbHwXGuWmO9_AFGFOeSXuZae4IsWEFYjcPxqfZI9i3CBUEsHYw-ykEIRVSNDT7NeXz-_yuVMxWmMhnOezPICzaukgV02dx31sYataq3M9UDr9-SZvvXe58SFvfBMhvZMt1Fa1UOc1aLXP4QqaNj7OHhjlIjwZvmfZjw_vv88_TS4uPy7ms4uJZlXRTkSNMCaaMIbrJcfEYI6gojXjiJWoomXCFOe6wIYgUy11wbgpDWMGF7gqGTnLnh90d85HOZgTJRaCiIImIxKxOBC1Vxu5C3arwl56ZeX1hA8rqUJK1IGsONIlYoJRYBRppQQSSBXA0zFKBr3W22G3bpnS1inToNxIdLzS2LVc-StZEp687wVeDQLB_-4gtnJrowbnVAO-uz43xaxMcEJf_IPend1ArVRKwDbGp311LypnNGGIUkQTNb2DSk8NW6tTJRmb5kcBr0cBiWnhT7tSXYxy8e3r_7OXP8fsyyN2Dcq16-hd15dWHIP0AOrgYwxgbk3GSPaNcOOG7BtBDo2Qwp4dX9Bt0E3lk7-oYQEa</recordid><startdate>20170403</startdate><enddate>20170403</enddate><creator>Hsu, Min-Kung</creator><creator>Lin, Hsuan-Yu</creator><creator>Chen, Feng-Chi</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-1437-4420</orcidid></search><sort><creationdate>20170403</creationdate><title>NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events</title><author>Hsu, Min-Kung ; Lin, Hsuan-Yu ; Chen, Feng-Chi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-8d0113c3661db713f170e94d670650945c69a77c21f30f9bc267f5f66f1219563</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Adenocarcinoma</topic><topic>Adenocarcinoma - metabolism</topic><topic>Adenocarcinoma of Lung</topic><topic>Alignment</topic><topic>Alternative Splicing</topic><topic>Annotations</topic><topic>Assembly</topic><topic>Bacteria</topic><topic>Biochemistry</topic><topic>Biodegradation</topic><topic>Bioinformatics</topic><topic>Biological activity</topic><topic>Biology and Life Sciences</topic><topic>Blood</topic><topic>Brain</topic><topic>Cell differentiation</topic><topic>Chromatin</topic><topic>Classification</topic><topic>Coding</topic><topic>Codons</topic><topic>Computer Simulation</topic><topic>Conserved sequence</topic><topic>Decay</topic><topic>Degradation</topic><topic>Dentistry</topic><topic>Differentiation</topic><topic>Dystrophy</topic><topic>Effectors</topic><topic>Eukaryotes</topic><topic>Evolution</topic><topic>Exons</topic><topic>Gene expression</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene regulation</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Health sciences</topic><topic>Humans</topic><topic>Internet</topic><topic>Kinases</topic><topic>Lung cancer</topic><topic>Lung Neoplasms - metabolism</topic><topic>Lungs</topic><topic>Mammals</topic><topic>Medical research</topic><topic>Medicine and Health Sciences</topic><topic>Messenger RNA</topic><topic>Movement disorders</topic><topic>Muscular dystrophy</topic><topic>Mutation</topic><topic>Neurodegenerative diseases</topic><topic>Nonsense Mediated mRNA Decay</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Parkinson's disease</topic><topic>Placenta</topic><topic>Protein kinase</topic><topic>Proteins</topic><topic>Quality control</topic><topic>Retention</topic><topic>Retinitis pigmentosa</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Simulation</topic><topic>Single nucleotide polymorphisms</topic><topic>Stop codon</topic><topic>Surveillance</topic><topic>Switching</topic><topic>T cell receptors</topic><topic>Technology</topic><topic>Transcription</topic><topic>Vertebrates</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hsu, Min-Kung</creatorcontrib><creatorcontrib>Lin, Hsuan-Yu</creatorcontrib><creatorcontrib>Chen, Feng-Chi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hsu, Min-Kung</au><au>Lin, Hsuan-Yu</au><au>Chen, Feng-Chi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-04-03</date><risdate>2017</risdate><volume>12</volume><issue>4</issue><spage>e0174798</spage><epage>e0174798</epage><pages>e0174798-e0174798</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28369084</pmid><doi>10.1371/journal.pone.0174798</doi><tpages>e0174798</tpages><orcidid>https://orcid.org/0000-0002-1437-4420</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2017-04, Vol.12 (4), p.e0174798-e0174798 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1883824932 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Adenocarcinoma Adenocarcinoma - metabolism Adenocarcinoma of Lung Alignment Alternative Splicing Annotations Assembly Bacteria Biochemistry Biodegradation Bioinformatics Biological activity Biology and Life Sciences Blood Brain Cell differentiation Chromatin Classification Coding Codons Computer Simulation Conserved sequence Decay Degradation Dentistry Differentiation Dystrophy Effectors Eukaryotes Evolution Exons Gene expression Gene Expression Profiling - methods Gene regulation Genetics Genomes Genomics Health sciences Humans Internet Kinases Lung cancer Lung Neoplasms - metabolism Lungs Mammals Medical research Medicine and Health Sciences Messenger RNA Movement disorders Muscular dystrophy Mutation Neurodegenerative diseases Nonsense Mediated mRNA Decay Nucleotide sequence Nucleotides Parkinson's disease Placenta Protein kinase Proteins Quality control Retention Retinitis pigmentosa Ribonucleic acid RNA Simulation Single nucleotide polymorphisms Stop codon Surveillance Switching T cell receptors Technology Transcription Vertebrates |
| title | NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-04T21%3A51%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=NMD%20Classifier:%20A%20reliable%20and%20systematic%20classification%20tool%20for%20nonsense-mediated%20decay%20events&rft.jtitle=PloS%20one&rft.au=Hsu,%20Min-Kung&rft.date=2017-04-03&rft.volume=12&rft.issue=4&rft.spage=e0174798&rft.epage=e0174798&rft.pages=e0174798-e0174798&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0174798&rft_dat=%3Cgale_plos_%3EA488304404%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1883824932&rft_id=info:pmid/28369084&rft_galeid=A488304404&rft_doaj_id=oai_doaj_org_article_970c506864e640caa8080a2e75c656e2&rfr_iscdi=true |