Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

• Published in: BMC genomics Vol. 21; no. 1; p. 690
• Main Authors: Levin, Michal, Scheibe, Marion, Butter, Falk
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 06-10-2020; BioMed Central; BMC
• Subjects: Animals; Annotations; Big data; Biotechnology; Bombyx - genetics; Bombyx - metabolism; Bombyx mori; Cloning; Consortia; CRISPR; Gene amplification; Gene annotation; Gene assembly; Gene expression; Genes; Genetic aspects; Genomes; Genomics; Insect Proteins - genetics; Insect Proteins - metabolism; Localization; Management; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Molecular biology; Molecular Sequence Annotation - methods; Nucleotide sequence; Observations; Peptides; Proteins; Proteogenomics - methods; Proteome; Proteomics; Proteotranscriptomics; Reading; Ribonucleic acid; RNA; Scientific imaging; Silkworms; Spatial proteomics; Spectroscopy; Transcription (Genetics); Transcriptome; Germany; Spatial proteomics; Mass spectrometry; Gene assembly; Gene annotation; Proteotranscriptomics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-07088-7

The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise.
Combining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage.
We show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.