Article (Scientific journals)
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms
Sheynkman, G. M.; Tuttle, K. S.; Laval, Florent et al.
2020In Nature Communications, 11 (1)
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Abstract :
[en] Most human protein-coding genes are expressed as multiple isoforms, which greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every coding gene, the majority of alternative isoforms remains uncharacterized due to (i) vast differences of overall levels between different isoforms expressed from common genes, and (ii) the difficulty of obtaining full-length transcript sequences. Here, we present ORF Capture-Seq (OCS), a flexible method that addresses both challenges for targeted full-length isoform sequencing applications using collections of cloned ORFs as probes. As a proof-of-concept, we show that an OCS pipeline focused on genes coding for transcription factors increases isoform detection by an order of magnitude when compared to unenriched samples. In short, OCS enables rapid discovery of isoforms from custom-selected genes and will accelerate mapping of the human transcriptome. © 2020, The Author(s).
Disciplines :
Biotechnology
Author, co-author :
Sheynkman, G. M.;  Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
Tuttle, K. S.;  Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Biochemistry, Northeastern University, Boston, MA 02115, United States, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States, Icahn Institute of Data Science and Genomic Technology, New York, NY 10029, United States
Laval, Florent  ;  Université de Liège - ULiège > Terra
Tseng, E.;  Pacific Biosciences, Menlo Park, CA 94025, United States
Underwood, J. G.;  Pacific Biosciences, Menlo Park, CA 94025, United States
Yu, L.;  School of Computer Science and Technology, Xidian University, Xi’an, 710071, China
Dong, D.;  School of Computer Science and Technology, Xidian University, Xi’an, 710071, China
Smith, M. L.;  Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States, Icahn Institute of Data Science and Genomic Technology, New York, NY 10029, United States
Sebra, R.;  Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States, Icahn Institute of Data Science and Genomic Technology, New York, NY 10029, United States
Willems, Luc  ;  Université de Liège - ULiège > Cancer-Cellular and Molecular Epigenetics
Hao, T.;  Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
Calderwood, M. A.;  Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
Hill, D. E.;  Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
Vidal, M.;  Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, United States, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
More authors (4 more) Less
Title :
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms
Publication date :
2020
Journal title :
Nature Communications
eISSN :
2041-1723
Publisher :
Nature Research
Volume :
11
Issue :
1
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
Melanoma Research Foundation, MRFBelgian American Educational Foundation, BAEFNational Institutes of Health, NIH: T32CA009361National Cancer Institute, NCI: U01CA232161P50HG004233
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