Dataset Information

Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing.

ABSTRACT: Alternative splicing (AS) isoforms create numerous proteoforms, expanding the complexity of the genome. Highly similar sequences, incomplete reference databases and the insufficient sequence coverage of mass spectrometry limit the identification of AS proteoforms. Here, we demonstrated full-length translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) sequencing (RNC-seq) strategy to sequence the entire translating mRNA using next-generation sequencing, including short-read and long-read technologies, to construct a protein database containing all translating AS isoforms. Taking the advantage of read length, short-read RNC-seq identified up to 15,289 genes and 15,906 AS isoforms in a single human cell line, much more than the Ribo-seq. The single-molecule long-read RNC-seq supplemented 4,429 annotated AS isoforms that were not identified by short-read datasets, and 4,525 novel AS isoforms that were not included in the public databases. Using such RNC-seq-guided database, we identified 6,766 annotated protein isoforms and 50 novel protein isoforms in mass spectrometry datasets. These results demonstrated the potential of full-length RNC-seq in investigating the proteome of AS isoforms.

SUBMITTER: Wu C

PROVIDER: S-EPMC9201276 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing.

Wu Chun C Lu Xiaolong X Lu Shaohua S Wang Hongwei H Li Dehua D Zhao Jing J Jin Jingjie J Sun Zhenghua Z He Qing-Yu QY Chen Yang Y Zhang Gong G

Frontiers in molecular biosciences 20220602

Alternative splicing (AS) isoforms create numerous proteoforms, expanding the complexity of the genome. Highly similar sequences, incomplete reference databases and the insufficient sequence coverage of mass spectrometry limit the identification of AS proteoforms. Here, we demonstrated full-length translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) sequencing (RNC-seq) strategy to sequence the entire translating mRNA using next-generation sequencing, including short-read an ...[more]

PMID: 35720116

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Dataset Information

Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing.

Publications

Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing.

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