Improved definition of the mouse transcriptome via targeted RNA sequencing
Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly....
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| Published in | Genome research Vol. 26; no. 5; pp. 705 - 716 |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Cold Spring Harbor Laboratory Press (CSHL Press)
01.05.2016
Cold Spring Harbor Laboratory Press |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1088-9051 1549-5469 1549-5469 |
| DOI | 10.1101/gr.199760.115 |
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| Abstract | Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources. |
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| AbstractList | Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.
The authors acknowledge the following funding sources: an Australian National Health and Medical Research Council (NHMRC) Australia Fellowship (631668 to J.S.M. and 631542 to M.E.D.); an NHMRC Early Career Fellowship (APP1072662 to M.B.C.); an EMBO Long Term Fellowship (ALTF 864-2013 to M.B.C.); an Australian National Health and Medical Research Council (NHMRC) Project Grant (APP1062106 to T.R.M.) and Career Development Fellowship (APP1062470 to T.R.M); and an EMBL Interdisciplinary Postdoc (EIPOD) under Marie Curie Actions (COFUND) (to G.B.). Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources. Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources. |
| Author | Leonardi, Tommaso Dinger, Marcel E. Mattick, John S. Bussotti, Giovanni Notredame, Cedric Crawford, Joanna Malquori, Lorenzo Enright, Anton J. Mercer, Tim R. Clark, Michael B. |
| AuthorAffiliation | 6 Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain 5 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia 3 MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom 4 St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia 2 Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia 1 EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom |
| AuthorAffiliation_xml | – name: 3 MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom – name: 1 EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom – name: 2 Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia – name: 4 St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia – name: 6 Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain – name: 5 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia |
| Author_xml | – sequence: 1 givenname: Giovanni orcidid: 0000-0002-4078-7413 surname: Bussotti fullname: Bussotti, Giovanni – sequence: 2 givenname: Tommaso orcidid: 0000-0002-4449-1863 surname: Leonardi fullname: Leonardi, Tommaso – sequence: 3 givenname: Michael B. surname: Clark fullname: Clark, Michael B. – sequence: 4 givenname: Tim R. surname: Mercer fullname: Mercer, Tim R. – sequence: 5 givenname: Joanna surname: Crawford fullname: Crawford, Joanna – sequence: 6 givenname: Lorenzo surname: Malquori fullname: Malquori, Lorenzo – sequence: 7 givenname: Cedric surname: Notredame fullname: Notredame, Cedric – sequence: 8 givenname: Marcel E. surname: Dinger fullname: Dinger, Marcel E. – sequence: 9 givenname: John S. surname: Mattick fullname: Mattick, John S. – sequence: 10 givenname: Anton J. orcidid: 0000-0002-6090-3100 surname: Enright fullname: Enright, Anton J. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27197243$$D View this record in MEDLINE/PubMed |
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| Copyright | 2016 Bussotti et al.; Published by Cold Spring Harbor Laboratory Press. info:eu-repo/semantics/openAccess © 2016 Bussotti et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. http://creativecommons.org/licenses/by/4.0 2016 |
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| SubjectTerms | Animals Gene Expression Profiling - methods Genètica High-Throughput Nucleotide Sequencing - methods Mice Ratolins Resource RNA RNA, Long Noncoding - biosynthesis RNA, Long Noncoding - genetics Transcriptome |
| Title | Improved definition of the mouse transcriptome via targeted RNA sequencing |
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