ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms

[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

More authors (4 more)

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 :

Issue :

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

Available on ORBi :

since 10 June 2020

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