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

ABSTRACT: 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.

SUBMITTER: Sheynkman GM

PROVIDER: S-EPMC7214433 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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

Sheynkman Gloria M GM Tuttle Katharine S KS Laval Florent F Tseng Elizabeth E Underwood Jason G JG Yu Liang L Dong Da D Smith Melissa L ML Sebra Robert R Willems Luc L Hao Tong T Calderwood Michael A MA Hill David E DE Vidal Marc M

Nature communications 20200511 1

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 Capt ...[more]

PMID: 32393825

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Dataset Information

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

Publications

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

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