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Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

Guttman, Mitchell and Garber, Manuel and Levin, Joshua Z. and Donaghey, Julie and Robinson, James and Adiconis, Xian and Fan, Lin and Koziol, Magdalena J. and Gnirke, Andreas and Nusbaum, Chad and Rinn, John L. and Lander, Eric S. and Regev, Aviv (2010) Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology, 28 (5). pp. 503-510. ISSN 1087-0156. PMCID PMC2868100. https://resolver.caltech.edu/CaltechAUTHORS:20161122-073633977

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Abstract

Massively parallel cDNA sequencing (RNA-Seq) provides an unbiased way to study a transcriptome, including both coding and noncoding genes. Until now, most RNA-Seq studies have depended crucially on existing annotations and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We applied it to mouse embryonic stem cells, neuronal precursor cells and lung fibroblasts to accurately reconstruct the full-length gene structures for most known expressed genes. We identified substantial variation in protein coding genes, including thousands of novel 5′ start sites, 3′ ends and internal coding exons. We then determined the gene structures of more than a thousand large intergenic noncoding RNA (lincRNA) and antisense loci. Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nbt.1633DOIArticle
http://www.nature.com/nbt/journal/v28/n5/full/nbt.1633.htmlPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868100/PubMed CentralArticle
http://dx.doi.org/10.1038/nbt0710-756b DOICorrigendum
http://rdcu.be/mRT9PublisherFree ReadCube access
ORCID:
AuthorORCID
Guttman, Mitchell0000-0003-4748-9352
Robinson, James0000-0001-9417-3938
Lander, Eric S.0000-0003-2662-4631
Regev, Aviv0000-0003-3293-3158
Additional Information:© 2010 Macmillan Publishers Limited. Received 10 March; accepted 6 April; published online 2 May 2010; corrected after print 9 July 2010. We thank M. Wernig (MIT) for providing NPC; M. Lin and M. Kellis (MIT) for CSF code; the Broad Sequencing Platform for sample sequencing; L. Gaffney for assistance with graphics; and C. Burge, J. Merkin, R. Bradley and members of Lander and Regev laboratories—in particular, M. Yassour, T. Mikkelsen and I. Amit—for discussions. A.R. and J.L.R. were supported by the Merkin Family Foundation for Stem Cell Research at the Broad Institute. M. Guttman was supported by a Vertex scholarship. Work was supported by a Burroughs Wellcome Fund Career Award at the Scientific Interface, a US National Institutes of Health PIONEER award, a US National Human Genome Research Institute (NHGRI) R01 grant and the Howard Hughes Medical Institute (A.R.), and NHGRI and the Broad Institute of MIT and Harvard (E.S.L.). Author Contributions: M. Guttman and M. Garber conceived the project, designed research, implemented Scripture, performed computational analysis and wrote the paper. A.G., C.N. and J.Z.L. oversaw cDNA sequencing, provided molecular biology advice and helped to edit the manuscript. J.D. constructed cDNA libraries, performed validation experiments and helped to edit the manuscript. J.R. implemented components of Scripture and provided computational support and technical advice. X.A., L.F. and M.J.K. constructed cDNA libraries. J.L.R. provided reagents and helped edit the manuscript. E.S.L. designed research direction and wrote the paper. A.R. provided cDNA sequencing guidance, conceived the project, designed research direction and wrote the paper. The authors declare no competing financial interests.
Funders:
Funding AgencyGrant Number
Broad Institute of MIT and HarvardUNSPECIFIED
Vertex ScholarshipUNSPECIFIED
Burroughs Wellcome FundUNSPECIFIED
NIHUNSPECIFIED
National Human Genome Research InstituteUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Issue or Number:5
PubMed Central ID:PMC2868100
Record Number:CaltechAUTHORS:20161122-073633977
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20161122-073633977
Official Citation:Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Mitchell Guttman, Manuel Garber, Joshua Z Levin, Julie Donaghey, James Robinson, Xian Adiconis, Lin Fan, Magdalena J Koziol, Andreas Gnirke, Chad Nusbaum, John L Rinn, Eric S Lander & Aviv Regev Nature Biotechnology 28, 503–510 (2010) doi:10.1038/nbt.1633
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:72232
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:22 Nov 2016 15:55
Last Modified:14 Oct 2019 17:56

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