uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames
Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within t...
Gespeichert in:
| Veröffentlicht in: | PloS one 2019-09, Vol.14 (9), p.e0222459-e0222459 |
|---|---|
| Hauptverfasser: | , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0222459 |
|---|---|
| container_issue | 9 |
| container_start_page | e0222459 |
| container_title | PloS one |
| container_volume | 14 |
| creator | Scholz, Anica Eggenhofer, Florian Gelhausen, Rick Grüning, Björn Zarnack, Kathi Brüne, Bernhard Backofen, Rolf Schmid, Tobias |
| description | Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5' untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources. |
| doi_str_mv | 10.1371/journal.pone.0222459 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_2289562977</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A599263209</galeid><doaj_id>oai_doaj_org_article_49a2a1380fb540198a48dc14691e8913</doaj_id><sourcerecordid>A599263209</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-beedd86ec30ab42e2e22bd3b05a5ef258304f784a022986ea964129a9fa773b83</originalsourceid><addsrcrecordid>eNqNk01v1DAQhiMEomXhHyCIhITgkMVf-fAFqaoorFRppVLgaCbJOJvixIudAP33ON202kU9IB8ysZ95PTOeiaLnlCwpz-m7Kzu6Hsxya3tcEsaYSOWD6JhKzpKMEf5wzz6Knnh_RUjKiyx7HB1xmlKeCXocfR_XF2fJpbXGJ9-s-6GN_R1r6-Jhg3GNA7qu7WFobR9bHQ8Oem9ufhOHzRhM667jcesHh9DFdot9HKy67ZtYO-jQP40eaTAen83fRfTl7MPl6afkfP1xdXpynlSZZENSItZ1kWHFCZSCYVisrHlJUkhRs7TgROi8EBAylYEDGcJnEqSGPOdlwRfRy53u1liv5uJ4xVgh04zJAC2i1Y6oLVyprWs7cNfKQqtuNqxrFLihrQwqIYEB5QXRZSoIlQWIoq6oyCTFQlIetN7Pt41lh3WFfSiNORA9POnbjWrsL5XlgomcBIE3s4CzP0f0g-paX6Ex0KMdp7glkaTgbIr71T_o_dnNVAMhgbbXNtxbTaLqJJWSZZwRGajlPVRYNXZtFTpJt2H_wOHtgUNgBvwzNDB6r1afL_6fXX89ZF_vsRsEM2y8NePUWv4QFDuwctZ7h_quyJSoaRBuq6GmQVDzIAS3F_sPdOd02_n8L4FWA1s</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2289562977</pqid></control><display><type>article</type><title>uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames</title><source>Public Library of Science (PLoS) Journals Open Access</source><source>PubMed (Medline)</source><source>MEDLINE</source><source>Directory of Open Access Journals</source><source>Free Full-Text Journals in Chemistry</source><source>EZB Electronic Journals Library</source><creator>Scholz, Anica ; Eggenhofer, Florian ; Gelhausen, Rick ; Grüning, Björn ; Zarnack, Kathi ; Brüne, Bernhard ; Backofen, Rolf ; Schmid, Tobias</creator><contributor>Jan, Eric</contributor><creatorcontrib>Scholz, Anica ; Eggenhofer, Florian ; Gelhausen, Rick ; Grüning, Björn ; Zarnack, Kathi ; Brüne, Bernhard ; Backofen, Rolf ; Schmid, Tobias ; Jan, Eric</creatorcontrib><description>Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5' untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0222459</identifier><identifier>PMID: 31513641</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>5' Untranslated Regions ; Amino acid sequence ; Analysis ; Annotations ; Biochemistry ; Bioinformatics ; Biology and Life Sciences ; Computer science ; Criminal investigation ; Endoplasmic reticulum ; Gene expression ; Gene Expression Profiling - methods ; Gene Expression Regulation ; Genomes ; Humans ; Identification ; Identification and classification ; Kinases ; Life sciences ; Messenger RNA ; Methods ; Occupancy ; Open reading frames ; Open Reading Frames - genetics ; Phosphorylation ; Protein Biosynthesis ; Protein Processing, Post-Translational ; Proteins ; Reading ; Regulation ; Ribosomes - genetics ; RNA sequencing ; RNA, Messenger ; Software ; Transcription ; Translation ; Translation (Genetics) ; Upstream ; Wavelet transforms ; Workflow ; Workflow software</subject><ispartof>PloS one, 2019-09, Vol.14 (9), p.e0222459-e0222459</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Scholz 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>2019 Scholz et al 2019 Scholz et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-beedd86ec30ab42e2e22bd3b05a5ef258304f784a022986ea964129a9fa773b83</citedby><cites>FETCH-LOGICAL-c692t-beedd86ec30ab42e2e22bd3b05a5ef258304f784a022986ea964129a9fa773b83</cites><orcidid>0000-0002-1952-5259</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/PMC6742470/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742470/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23871,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31513641$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Jan, Eric</contributor><creatorcontrib>Scholz, Anica</creatorcontrib><creatorcontrib>Eggenhofer, Florian</creatorcontrib><creatorcontrib>Gelhausen, Rick</creatorcontrib><creatorcontrib>Grüning, Björn</creatorcontrib><creatorcontrib>Zarnack, Kathi</creatorcontrib><creatorcontrib>Brüne, Bernhard</creatorcontrib><creatorcontrib>Backofen, Rolf</creatorcontrib><creatorcontrib>Schmid, Tobias</creatorcontrib><title>uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5' untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.</description><subject>5' Untranslated Regions</subject><subject>Amino acid sequence</subject><subject>Analysis</subject><subject>Annotations</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Computer science</subject><subject>Criminal investigation</subject><subject>Endoplasmic reticulum</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation</subject><subject>Genomes</subject><subject>Humans</subject><subject>Identification</subject><subject>Identification and classification</subject><subject>Kinases</subject><subject>Life sciences</subject><subject>Messenger RNA</subject><subject>Methods</subject><subject>Occupancy</subject><subject>Open reading frames</subject><subject>Open Reading Frames - genetics</subject><subject>Phosphorylation</subject><subject>Protein Biosynthesis</subject><subject>Protein Processing, Post-Translational</subject><subject>Proteins</subject><subject>Reading</subject><subject>Regulation</subject><subject>Ribosomes - genetics</subject><subject>RNA sequencing</subject><subject>RNA, Messenger</subject><subject>Software</subject><subject>Transcription</subject><subject>Translation</subject><subject>Translation (Genetics)</subject><subject>Upstream</subject><subject>Wavelet transforms</subject><subject>Workflow</subject><subject>Workflow software</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk01v1DAQhiMEomXhHyCIhITgkMVf-fAFqaoorFRppVLgaCbJOJvixIudAP33ON202kU9IB8ysZ95PTOeiaLnlCwpz-m7Kzu6Hsxya3tcEsaYSOWD6JhKzpKMEf5wzz6Knnh_RUjKiyx7HB1xmlKeCXocfR_XF2fJpbXGJ9-s-6GN_R1r6-Jhg3GNA7qu7WFobR9bHQ8Oem9ufhOHzRhM667jcesHh9DFdot9HKy67ZtYO-jQP40eaTAen83fRfTl7MPl6afkfP1xdXpynlSZZENSItZ1kWHFCZSCYVisrHlJUkhRs7TgROi8EBAylYEDGcJnEqSGPOdlwRfRy53u1liv5uJ4xVgh04zJAC2i1Y6oLVyprWs7cNfKQqtuNqxrFLihrQwqIYEB5QXRZSoIlQWIoq6oyCTFQlIetN7Pt41lh3WFfSiNORA9POnbjWrsL5XlgomcBIE3s4CzP0f0g-paX6Ex0KMdp7glkaTgbIr71T_o_dnNVAMhgbbXNtxbTaLqJJWSZZwRGajlPVRYNXZtFTpJt2H_wOHtgUNgBvwzNDB6r1afL_6fXX89ZF_vsRsEM2y8NePUWv4QFDuwctZ7h_quyJSoaRBuq6GmQVDzIAS3F_sPdOd02_n8L4FWA1s</recordid><startdate>20190912</startdate><enddate>20190912</enddate><creator>Scholz, Anica</creator><creator>Eggenhofer, Florian</creator><creator>Gelhausen, Rick</creator><creator>Grüning, Björn</creator><creator>Zarnack, Kathi</creator><creator>Brüne, Bernhard</creator><creator>Backofen, Rolf</creator><creator>Schmid, Tobias</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>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>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-1952-5259</orcidid></search><sort><creationdate>20190912</creationdate><title>uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames</title><author>Scholz, Anica ; Eggenhofer, Florian ; Gelhausen, Rick ; Grüning, Björn ; Zarnack, Kathi ; Brüne, Bernhard ; Backofen, Rolf ; Schmid, Tobias</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-beedd86ec30ab42e2e22bd3b05a5ef258304f784a022986ea964129a9fa773b83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>5' Untranslated Regions</topic><topic>Amino acid sequence</topic><topic>Analysis</topic><topic>Annotations</topic><topic>Biochemistry</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Computer science</topic><topic>Criminal investigation</topic><topic>Endoplasmic reticulum</topic><topic>Gene expression</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Regulation</topic><topic>Genomes</topic><topic>Humans</topic><topic>Identification</topic><topic>Identification and classification</topic><topic>Kinases</topic><topic>Life sciences</topic><topic>Messenger RNA</topic><topic>Methods</topic><topic>Occupancy</topic><topic>Open reading frames</topic><topic>Open Reading Frames - genetics</topic><topic>Phosphorylation</topic><topic>Protein Biosynthesis</topic><topic>Protein Processing, Post-Translational</topic><topic>Proteins</topic><topic>Reading</topic><topic>Regulation</topic><topic>Ribosomes - genetics</topic><topic>RNA sequencing</topic><topic>RNA, Messenger</topic><topic>Software</topic><topic>Transcription</topic><topic>Translation</topic><topic>Translation (Genetics)</topic><topic>Upstream</topic><topic>Wavelet transforms</topic><topic>Workflow</topic><topic>Workflow software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Scholz, Anica</creatorcontrib><creatorcontrib>Eggenhofer, Florian</creatorcontrib><creatorcontrib>Gelhausen, Rick</creatorcontrib><creatorcontrib>Grüning, Björn</creatorcontrib><creatorcontrib>Zarnack, Kathi</creatorcontrib><creatorcontrib>Brüne, Bernhard</creatorcontrib><creatorcontrib>Backofen, Rolf</creatorcontrib><creatorcontrib>Schmid, Tobias</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>ProQuest Nursing and Allied Health Journals</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>ProQuest 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)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Database (1962 - current)</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>ProQuest 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</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 (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>https://resources.nclive.org/materials</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>PML(ProQuest Medical Library)</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>ProQuest advanced technologies & aerospace journals</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 (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</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>Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Scholz, Anica</au><au>Eggenhofer, Florian</au><au>Gelhausen, Rick</au><au>Grüning, Björn</au><au>Zarnack, Kathi</au><au>Brüne, Bernhard</au><au>Backofen, Rolf</au><au>Schmid, Tobias</au><au>Jan, Eric</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2019-09-12</date><risdate>2019</risdate><volume>14</volume><issue>9</issue><spage>e0222459</spage><epage>e0222459</epage><pages>e0222459-e0222459</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5' untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>31513641</pmid><doi>10.1371/journal.pone.0222459</doi><tpages>e0222459</tpages><orcidid>https://orcid.org/0000-0002-1952-5259</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2019-09, Vol.14 (9), p.e0222459-e0222459 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2289562977 |
| source | Public Library of Science (PLoS) Journals Open Access; PubMed (Medline); MEDLINE; Directory of Open Access Journals; Free Full-Text Journals in Chemistry; EZB Electronic Journals Library |
| subjects | 5' Untranslated Regions Amino acid sequence Analysis Annotations Biochemistry Bioinformatics Biology and Life Sciences Computer science Criminal investigation Endoplasmic reticulum Gene expression Gene Expression Profiling - methods Gene Expression Regulation Genomes Humans Identification Identification and classification Kinases Life sciences Messenger RNA Methods Occupancy Open reading frames Open Reading Frames - genetics Phosphorylation Protein Biosynthesis Protein Processing, Post-Translational Proteins Reading Regulation Ribosomes - genetics RNA sequencing RNA, Messenger Software Transcription Translation Translation (Genetics) Upstream Wavelet transforms Workflow Workflow software |
| title | uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-13T20%3A41%3A59IST&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=uORF-Tools-Workflow%20for%20the%20determination%20of%20translation-regulatory%20upstream%20open%20reading%20frames&rft.jtitle=PloS%20one&rft.au=Scholz,%20Anica&rft.date=2019-09-12&rft.volume=14&rft.issue=9&rft.spage=e0222459&rft.epage=e0222459&rft.pages=e0222459-e0222459&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0222459&rft_dat=%3Cgale_plos_%3EA599263209%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=2289562977&rft_id=info:pmid/31513641&rft_galeid=A599263209&rft_doaj_id=oai_doaj_org_article_49a2a1380fb540198a48dc14691e8913&rfr_iscdi=true |