Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Identifieur interne : 000414 ( Main/Exploration ); précédent : 000413; suivant : 000415Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Auteurs : Tobias Neumann [Autriche] ; Veronika A. Herzog [Autriche] ; Matthias Muhar [Autriche] ; Arndt Von Haeseler [Autriche] ; Johannes Zuber [Autriche] ; Stefan L. Ameres [Autriche] ; Philipp Rescheneder [Autriche]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Nucleotides.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA.
- Polymorphism, Single Nucleotide, Software.
Abstract
Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretation of such events in high-throughput sequencing datasets demands specialized bioinformatics approaches.
Here, we present Digital Unmasking of Nucleotide conversions in K-mers (DUNK), a data analysis pipeline enabling the quantification of nucleotide conversions in high-throughput sequencing datasets. We demonstrate using experimentally generated and simulated datasets that DUNK allows constant mapping rates irrespective of nucleotide-conversion rates, promotes the recovery of multimapping reads and employs Single Nucleotide Polymorphism (SNP) masking to uncouple true SNPs from nucleotide conversions to facilitate a robust and sensitive quantification of nucleotide-conversions. As a first application, we implement this strategy as SLAM-DUNK for the analysis of SLAMseq profiles, in which 4-thiouridine-labeled transcripts are detected based on T > C conversions. SLAM-DUNK provides both raw counts of nucleotide-conversion containing reads as well as a base-content and read coverage normalized approach for estimating the fractions of labeled transcripts as readout.
Beyond providing a readily accessible tool for analyzing SLAMseq and related time-resolved RNA sequencing methods (TimeLapse-seq, TUC-seq), DUNK establishes a broadly applicable strategy for quantifying nucleotide conversions.
The online version of this article (10.1186/s12859-019-2849-7) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-019-2849-7
PubMed: 31109287
PubMed Central: 6528199
Affiliations:
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Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, VBC, 1030 Vienna, Austria</nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, VBC, 1030 Vienna</wicri:regionArea><placeName><region type="land" nuts="2">Vienne (Autriche)</region><settlement type="city">Vienne (Autriche)</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Nucleotides (analysis)</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, RNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ARN ()</term><term>Logiciel</term><term>Nucléotides (analyse)</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage nucléotidique à haut débit ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Nucleotides</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Nucléotides</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Polymorphism, Single Nucleotide</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p id="Par1">Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretation of such events in high-throughput sequencing datasets demands specialized bioinformatics approaches.</p></sec><sec><title>Results</title><p id="Par2">Here, we present Digital Unmasking of Nucleotide conversions in K-mers (DUNK), a data analysis pipeline enabling the quantification of nucleotide conversions in high-throughput sequencing datasets. We demonstrate using experimentally generated and simulated datasets that DUNK allows constant mapping rates irrespective of nucleotide-conversion rates, promotes the recovery of multimapping reads and employs Single Nucleotide Polymorphism (SNP) masking to uncouple true SNPs from nucleotide conversions to facilitate a robust and sensitive quantification of nucleotide-conversions. As a first application, we implement this strategy as SLAM-DUNK for the analysis of SLAMseq profiles, in which 4-thiouridine-labeled transcripts are detected based on T > C conversions. SLAM-DUNK provides both raw counts of nucleotide-conversion containing reads as well as a base-content and read coverage normalized approach for estimating the fractions of labeled transcripts as readout.</p></sec><sec><title>Conclusion</title><p id="Par3">Beyond providing a readily accessible tool for analyzing SLAMseq and related time-resolved RNA sequencing methods (TimeLapse-seq, TUC-seq), DUNK establishes a broadly applicable strategy for quantifying nucleotide conversions.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12859-019-2849-7) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Frommer, M" uniqKey="Frommer M">M Frommer</name></author><author><name sortKey="Mcdonald, Le" uniqKey="Mcdonald L">LE McDonald</name></author><author><name sortKey="Millar, Ds" uniqKey="Millar D">DS Millar</name></author><author><name sortKey="Collis, Cm" uniqKey="Collis C">CM Collis</name></author><author><name sortKey="Watt, F" uniqKey="Watt F">F Watt</name></author><author><name sortKey="Grigg, Gw" uniqKey="Grigg G">GW Grigg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hafner, M" uniqKey="Hafner M">M Hafner</name></author><author><name sortKey="Landthaler, M" uniqKey="Landthaler M">M Landthaler</name></author><author><name sortKey="Burger, L" uniqKey="Burger L">L Burger</name></author><author><name sortKey="Khorshid, M" uniqKey="Khorshid M">M Khorshid</name></author><author><name sortKey="Hausser, J" uniqKey="Hausser J">J Hausser</name></author><author><name sortKey="Berninger, P" uniqKey="Berninger P">P Berninger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Xiong, X" uniqKey="Xiong X">X Xiong</name></author><author><name sortKey="Yi, C" uniqKey="Yi C">C Yi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Herzog, Va" uniqKey="Herzog V">VA Herzog</name></author><author><name sortKey="Reichholf, B" uniqKey="Reichholf B">B Reichholf</name></author><author><name sortKey="Neumann, T" uniqKey="Neumann T">T Neumann</name></author><author><name sortKey="Rescheneder, P" uniqKey="Rescheneder P">P Rescheneder</name></author><author><name sortKey="Bhat, P" uniqKey="Bhat P">P Bhat</name></author><author><name sortKey="Burkard, Tr" uniqKey="Burkard T">TR Burkard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Muhar, M" uniqKey="Muhar M">M Muhar</name></author><author><name sortKey="Ebert, A" uniqKey="Ebert A">A Ebert</name></author><author><name sortKey="Neumann, T" uniqKey="Neumann T">T Neumann</name></author><author><name sortKey="Umkehrer, C" uniqKey="Umkehrer C">C Umkehrer</name></author><author><name sortKey="Jude, J" uniqKey="Jude J">J Jude</name></author><author><name sortKey="Wieshofer, C" uniqKey="Wieshofer C">C Wieshofer</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Sedlazeck, Fj" uniqKey="Sedlazeck F">FJ Sedlazeck</name></author><author><name sortKey="Rescheneder, P" uniqKey="Rescheneder P">P Rescheneder</name></author><author><name sortKey="Haeseler, V A" uniqKey="Haeseler V">v A Haeseler</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Mignone, F" uniqKey="Mignone F">F Mignone</name></author><author><name sortKey="Gissi, C" uniqKey="Gissi C">C Gissi</name></author><author><name sortKey="Liuni, S" uniqKey="Liuni S">S Liuni</name></author><author><name sortKey="Pesole, G" uniqKey="Pesole G">G Pesole</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Young, Ra" uniqKey="Young R">RA 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Larson</name></author><author><name sortKey="Shen, D" uniqKey="Shen D">D Shen</name></author><author><name sortKey="Mclellan, Md" uniqKey="Mclellan M">MD McLellan</name></author><author><name sortKey="Lin, L" uniqKey="Lin L">L Lin</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Autriche</li></country><region><li>Vienne (Autriche)</li></region><settlement><li>Vienne (Autriche)</li></settlement></list><tree><country name="Autriche"><noRegion><name sortKey="Neumann, Tobias" sort="Neumann, Tobias" uniqKey="Neumann T" first="Tobias" last="Neumann">Tobias Neumann</name></noRegion><name sortKey="Ameres, Stefan L" sort="Ameres, Stefan L" uniqKey="Ameres S" first="Stefan L." last="Ameres">Stefan L. Ameres</name><name sortKey="Herzog, Veronika A" sort="Herzog, Veronika A" uniqKey="Herzog V" first="Veronika A." last="Herzog">Veronika A. Herzog</name><name sortKey="Muhar, Matthias" sort="Muhar, Matthias" uniqKey="Muhar M" first="Matthias" last="Muhar">Matthias Muhar</name><name sortKey="Rescheneder, Philipp" sort="Rescheneder, Philipp" uniqKey="Rescheneder P" first="Philipp" last="Rescheneder">Philipp Rescheneder</name><name sortKey="Von Haeseler, Arndt" sort="Von Haeseler, Arndt" uniqKey="Von Haeseler A" first="Arndt" last="Von Haeseler">Arndt Von Haeseler</name><name sortKey="Von Haeseler, Arndt" sort="Von Haeseler, Arndt" uniqKey="Von Haeseler A" first="Arndt" last="Von Haeseler">Arndt Von Haeseler</name><name sortKey="Zuber, Johannes" sort="Zuber, Johannes" uniqKey="Zuber J" first="Johannes" last="Zuber">Johannes Zuber</name><name sortKey="Zuber, Johannes" sort="Zuber, Johannes" uniqKey="Zuber J" first="Johannes" last="Zuber">Johannes Zuber</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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